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My Polarizable Water (PW) beads are bending after EM
- jimmy_chang
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6 years 3 months ago #7471
by jimmy_chang
My Polarizable Water (PW) beads are bending after EM was created by jimmy_chang
Hi there.
I seem to have a little bit of a problem during my EM process, and I really need some help.
Currently, I am trying to observe the self-assembly tendency of hydrophobin proteins. Here's my MARINI simulation process:
1. To start off I first martinized a monomer protein using the following command:
python martinize.py -f Protein.pdb -ss Protein.dssp -ff martini22p -p backbone -o topol.top -x Protein_CG.pdb
(It should be noted that my original all-atom monomer protein had 70 residues consisting 1010 atoms. After martinizing, it was reduced to 171 atoms). martinize.py was version 2.6
2. Then, I added my .itp files in my topology, which were: "martini_v2.2refP.itp," "martini_v2.2p_aminoacids," and "martini_v2.0_ions.itp" (The .itp files were from www.cgmartini.nl/index.php/force-field-p...particle-definitions
www.cgmartini.nl/index.php/force-field-parameters/amino-acids
and www.cgmartini.nl/index.php/force-field-parameters/ions )
3. I created my .gro file:
gmx editconf -f Protein_CG.pdb -c -d 1.5 -bt cubic -o Protein_CG.gro
The resulting box dimensions here were: [6.13912 6.13912 6.13912].
4. I ran a vacuum EM on this monomer:
gmx grompp -f VacuumEM.mdp -c Protein_CG.gro -p topol.top -o VacuumEM.tpr -maxwarn 1
The flag 'maxwarn 1' was for the atom name mismatch on SCD-SCN and SCD-SCP. My VacuumEM.mdp is:
You can see that my lincs-order and lincs-iter is pretty high, but I did not want to have any LINCS error during this process so I raised the value a bit. Anyways, from here I got my VacuumEM.gro file
5. After that I replicated my energy minimized structure using genconf:
gmx genconf -f VacuumEM.gro -nbox 4 4 3 -o 48-Mer.gro
This created a new box with dimensions [24.55648 24.55648 18.41736].
6. Then I solvated my system with polarizable water. First I used the following command to solvate with non-polarizable water:
gmx solvate -cp 48-Mer.gro -cs water.gro -p topol.top -o solv.gro -radius 0.21
and then ran python triple-w.py solv.gro to convert non-polarizable water to polar waters. This gave me the result gro file solv_PW.gro.
(I got water.gro and triple-w.py from www.cgmartini.nl/index.php/example-appli...ons2/solvent-systems and www.cgmartini.nl/index.php/tools2/resolution-transformation )
7. Since my system had no net charge, I skipped my ionization process and began running EM. In prior to creating a .tpr file, I read a post saying that the minimization process works better to use stiff bonds on PW molecules rather than constraints. So I have I have commented the [constraints] section and uncommented the [bonds] section:
After that, I ran an EM using 12 core workstation:
gmx grompp -f EM.mdp -c solv_PW.gro -p topol.top -o EM.tpr
mpirun -np 12 -host node01 mdrun_mpi -v -deffnm EM
Here is the EM.mdp file:
It's almost the same as VacuumEM.mdp, but I changed the 'periodic-molecules' as 'yes' along with emstep of 0.002
I anticipated my EM simulation to last a bit longer, but it finished very quickly with the following results:
8. I changed my PW stiff bonds to constraints again:
and tried to run my EQ with 10fs first.
gmx grompp -f EQ.mdp -c EM.gro -p topol.top -o EQ10.tpr
mpirun -np 12 -host node02 mdrun_mpi -v -deffnm EQ10
This is my EQ.mdp:
However, my system crashes with the following error:
Now, when I checked these LINCS erred molecules from EM.gro, I noticed that the water molecules were bent during EM
Does anyone know why this is happening? I looked up various things but I just can't seem to find out the solution.
Oh FYI, here are my topology and Protein_A.itp files:
topol.top
Protein_A.itp
Thank you very much in advance!
P.S I really wanted to upload the water molecules but I can't seem to find a way... if any knows how to upload an image please let me know!
I seem to have a little bit of a problem during my EM process, and I really need some help.
Currently, I am trying to observe the self-assembly tendency of hydrophobin proteins. Here's my MARINI simulation process:
1. To start off I first martinized a monomer protein using the following command:
python martinize.py -f Protein.pdb -ss Protein.dssp -ff martini22p -p backbone -o topol.top -x Protein_CG.pdb
(It should be noted that my original all-atom monomer protein had 70 residues consisting 1010 atoms. After martinizing, it was reduced to 171 atoms). martinize.py was version 2.6
2. Then, I added my .itp files in my topology, which were: "martini_v2.2refP.itp," "martini_v2.2p_aminoacids," and "martini_v2.0_ions.itp" (The .itp files were from www.cgmartini.nl/index.php/force-field-p...particle-definitions
www.cgmartini.nl/index.php/force-field-parameters/amino-acids
and www.cgmartini.nl/index.php/force-field-parameters/ions )
3. I created my .gro file:
gmx editconf -f Protein_CG.pdb -c -d 1.5 -bt cubic -o Protein_CG.gro
The resulting box dimensions here were: [6.13912 6.13912 6.13912].
4. I ran a vacuum EM on this monomer:
gmx grompp -f VacuumEM.mdp -c Protein_CG.gro -p topol.top -o VacuumEM.tpr -maxwarn 1
The flag 'maxwarn 1' was for the atom name mismatch on SCD-SCN and SCD-SCP. My VacuumEM.mdp is:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
; MARTINI EM mdp
; RUN CONTROL PARAMETERS
integrator = steep
nsteps = 10000000
; ENERGY MINIMIZATION OPTIONS
emtol = 1
emstep = 0.03
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = no
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
fourierspacing = 0.16
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = Lincs
continuation = no
lincs-order = 6
lincs-iter = 8
lincs-warnangle = 90
morse = no
; RUN CONTROL PARAMETERS
integrator = steep
nsteps = 10000000
; ENERGY MINIMIZATION OPTIONS
emtol = 1
emstep = 0.03
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = no
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
fourierspacing = 0.16
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = Lincs
continuation = no
lincs-order = 6
lincs-iter = 8
lincs-warnangle = 90
morse = no
You can see that my lincs-order and lincs-iter is pretty high, but I did not want to have any LINCS error during this process so I raised the value a bit. Anyways, from here I got my VacuumEM.gro file
5. After that I replicated my energy minimized structure using genconf:
gmx genconf -f VacuumEM.gro -nbox 4 4 3 -o 48-Mer.gro
This created a new box with dimensions [24.55648 24.55648 18.41736].
6. Then I solvated my system with polarizable water. First I used the following command to solvate with non-polarizable water:
gmx solvate -cp 48-Mer.gro -cs water.gro -p topol.top -o solv.gro -radius 0.21
and then ran python triple-w.py solv.gro to convert non-polarizable water to polar waters. This gave me the result gro file solv_PW.gro.
(I got water.gro and triple-w.py from www.cgmartini.nl/index.php/example-appli...ons2/solvent-systems and www.cgmartini.nl/index.php/tools2/resolution-transformation )
7. Since my system had no net charge, I skipped my ionization process and began running EM. In prior to creating a .tpr file, I read a post saying that the minimization process works better to use stiff bonds on PW molecules rather than constraints. So I have I have commented the [constraints] section and uncommented the [bonds] section:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;;;;;; POLARIZABLE WATER
[ moleculetype ]
; molname nrexcl
PW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 PW W 1 0
2 D 1 PW WP 1 0.457
3 D 1 PW WM 1 -0.457
;[constraints]
; i j funct length
; 1 2 1 0.14
; 1 3 1 0.14
; for minimization purposes constraints might be replaced by stiff bonds:
;
[bonds]
; i j funct length force const.
1 2 1 0.14 50000
1 3 1 0.14 50000
[angles]
; i j k funct angle fc
2 1 3 2 0.0 4.20
[exclusions]
1 2 3
2 3
[ moleculetype ]
; molname nrexcl
PW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 PW W 1 0
2 D 1 PW WP 1 0.457
3 D 1 PW WM 1 -0.457
;[constraints]
; i j funct length
; 1 2 1 0.14
; 1 3 1 0.14
; for minimization purposes constraints might be replaced by stiff bonds:
;
[bonds]
; i j funct length force const.
1 2 1 0.14 50000
1 3 1 0.14 50000
[angles]
; i j k funct angle fc
2 1 3 2 0.0 4.20
[exclusions]
1 2 3
2 3
After that, I ran an EM using 12 core workstation:
gmx grompp -f EM.mdp -c solv_PW.gro -p topol.top -o EM.tpr
mpirun -np 12 -host node01 mdrun_mpi -v -deffnm EM
Here is the EM.mdp file:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
; MARTINI EM mdp
; RUN CONTROL PARAMETERS
integrator = steep
nsteps = 1000000
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 1
emstep = 0.02
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
energygrp-table =
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = Lincs
continuation = no
lincs-order = 6
lincs-iter = 8
lincs-warnangle = 90
morse = no
; RUN CONTROL PARAMETERS
integrator = steep
nsteps = 1000000
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 1
emstep = 0.02
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
energygrp-table =
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = Lincs
continuation = no
lincs-order = 6
lincs-iter = 8
lincs-warnangle = 90
morse = no
It's almost the same as VacuumEM.mdp, but I changed the 'periodic-molecules' as 'yes' along with emstep of 0.002
I anticipated my EM simulation to last a bit longer, but it finished very quickly with the following results:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
Reading file EM.tpr, VERSION 5.0.7 (single precision)
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound.
Using 12 MPI processes
Using 1 OpenMP thread per MPI process
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 1000000
Step= 1, Dmax= 2.0e-02 nm, Epot= 1.90451e+08 Fmax= 2.44944e+06, atom= 175816
Step= 2, Dmax= 2.4e-02 nm, Epot= 6.43701e+07 Fmax= 1.52626e+06, atom= 196384
Step= 3, Dmax= 2.9e-02 nm, Epot= 5.91327e+07 Fmax= 8.43390e+05, atom= 192622
Step= 4, Dmax= 3.5e-02 nm, Epot= 5.39166e+07 Fmax= 5.20126e+05, atom= 192622
Step= 5, Dmax= 4.1e-02 nm, Epot= 4.96397e+07 Fmax= 3.50098e+05, atom= 192622
Step= 6, Dmax= 5.0e-02 nm, Epot= 4.61091e+07 Fmax= 1.15601e+05, atom= 231673
Step= 7, Dmax= 6.0e-02 nm, Epot= 3.95424e+07 Fmax= 1.56992e+05, atom= 128494
Step= 8, Dmax= 7.2e-02 nm, Epot= 3.57250e+07 Fmax= 5.88842e+04, atom= 128494
Step= 9, Dmax= 8.6e-02 nm, Epot= 2.62977e+07 Fmax= 1.02830e+05, atom= 181414
Step= 10, Dmax= 1.0e-01 nm, Epot= 2.17935e+07 Fmax= 2.99199e+04, atom= 258667
Step= 11, Dmax= 1.2e-01 nm, Epot= 1.82795e+07 Fmax= 2.14777e+07, atom= 262999
Step= 12, Dmax= 1.5e-01 nm, Epot= 1.01348e+07 Fmax= 5.17950e+05, atom= 174850
Step= 13, Dmax= 1.8e-01 nm, Epot= 1.00916e+07 Fmax= 1.87394e+06, atom= 180712
Step= 15, Dmax= 1.1e-01 nm, Epot= 9.40811e+06 Fmax= 3.43997e+05, atom= 180796
Step= 16, Dmax= 1.3e-01 nm, Epot= 8.85990e+06 Fmax= 3.60427e+04, atom= 180712
Step= 17, Dmax= 1.5e-01 nm, Epot= 4.59610e+06 Fmax= 4.47303e+04, atom= 158683
Step= 18, Dmax= 1.8e-01 nm, Epot= 2.57688e+06 Fmax= 3.06011e+05, atom= 175957
Step= 19, Dmax= 2.2e-01 nm, Epot= 2.41846e+06 Fmax= 1.22072e+07, atom= 158449
Step= 20, Dmax= 2.7e-01 nm, Epot= 2.19273e+06 Fmax= 1.65943e+05, atom= 180796
Step= 22, Dmax= 1.6e-01 nm, Epot= 1.86155e+06 Fmax= 4.61232e+05, atom= 163252
Step= 23, Dmax= 1.9e-01 nm, Epot= 1.71725e+06 Fmax= 2.74171e+04, atom= 157939
Step= 24, Dmax= 2.3e-01 nm, Epot= -1.23455e+05 Fmax= 4.00929e+05, atom= 43105
Step= 25, Dmax= 2.8e-01 nm, Epot= -2.08801e+05 Fmax= 8.84382e+05, atom= 43141
Step= 27, Dmax= 1.7e-01 nm, Epot= -2.22478e+05 Fmax= 7.37672e+05, atom= 43165
Step= 28, Dmax= 2.0e-01 nm, Epot= -2.29679e+05 Fmax= 1.99829e+06, atom= 38266
Step= 29, Dmax= 2.4e-01 nm, Epot= -2.78607e+05 Fmax= 7.14295e+04, atom= 38014
Step= 31, Dmax= 1.4e-01 nm, Epot= -4.46680e+05 Fmax= 2.06317e+05, atom= 43165
Step= 32, Dmax= 1.7e-01 nm, Epot= -5.06935e+05 Fmax= 1.14465e+05, atom= 37783
Step= 33, Dmax= 2.1e-01 nm, Epot= -6.11429e+05 Fmax= 1.76188e+05, atom= 39562
Step= 34, Dmax= 2.5e-01 nm, Epot= -6.94368e+05 Fmax= 4.90580e+04, atom= 37825
Step= 35, Dmax= 3.0e-01 nm, Epot= -8.97818e+05 Fmax= 1.83963e+06, atom= 37738
Step= 39, Dmax= 4.5e-02 nm, Epot= -9.23256e+05 Fmax= 8.12806e+05, atom= 43063
Step= 40, Dmax= 5.3e-02 nm, Epot= -9.41430e+05 Fmax= 2.21647e+05, atom= 37738
Step= 41, Dmax= 6.4e-02 nm, Epot= -9.54382e+05 Fmax= 8.79543e+04, atom= 43063
Step= 42, Dmax= 7.7e-02 nm, Epot= -9.79611e+05 Fmax= 1.58182e+04, atom= 43063
Step= 43, Dmax= 9.2e-02 nm, Epot= -1.10067e+06 Fmax= 1.20433e+04, atom= 37738
Step= 44, Dmax= 1.1e-01 nm, Epot= -1.20555e+06 Fmax= 1.43168e+04, atom= 43063
Step= 45, Dmax= 1.3e-01 nm, Epot= -1.25933e+06 Fmax= 9.65520e+03, atom= 43063
Step= 46, Dmax= 1.6e-01 nm, Epot= -1.31272e+06 Fmax= 4.06038e+04, atom= 43165
Step= 47, Dmax= 1.9e-01 nm, Epot= -1.32592e+06 Fmax= 4.51899e+04, atom= 38014
Step= 48, Dmax= 2.3e-01 nm, Epot= -1.34017e+06 Fmax= 1.32744e+04, atom= 37291
Step= 49, Dmax= 2.8e-01 nm, Epot= -1.37885e+06 Fmax= 4.62811e+04, atom= 37825
Step= 50, Dmax= 3.3e-01 nm, Epot= -1.39333e+06 Fmax= 3.04440e+04, atom= 37825
Step= 52, Dmax= 2.0e-01 nm, Epot= -1.40350e+06 Fmax= 3.62033e+04, atom= 43063
Step= 54, Dmax= 1.2e-01 nm, Epot= -1.40869e+06 Fmax= 2.70381e+04, atom= 43105
Step= 55, Dmax= 1.4e-01 nm, Epot= -1.41608e+06 Fmax= 2.07082e+04, atom= 37678
Step= 56, Dmax= 1.7e-01 nm, Epot= -1.42712e+06 Fmax= 1.02487e+04, atom= 37678
Step 57, time 0.057 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.340871, max 5.652700 (between atoms 59 and 60)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
59 60 168.5 0.1100 0.7318 0.1100
Back Off! I just backed up step57b_n0.pdb to ./#step57b_n0.pdb.1#
Back Off! I just backed up step57c_n0.pdb to ./#step57c_n0.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 58, Dmax= 1.0e-01 nm, Epot= -1.43984e+06 Fmax= 4.84458e+03, atom= 37288
Step= 59, Dmax= 1.2e-01 nm, Epot= -1.46546e+06 Fmax= 2.01342e+04, atom= 37288
Step= 60, Dmax= 1.5e-01 nm, Epot= -1.47391e+06 Fmax= 7.85587e+03, atom= 37288
Step= 61, Dmax= 1.8e-01 nm, Epot= -1.49067e+06 Fmax= 2.49859e+04, atom= 37288
Step= 62, Dmax= 2.1e-01 nm, Epot= -1.49833e+06 Fmax= 3.29761e+04, atom= 43072
Step= 64, Dmax= 1.3e-01 nm, Epot= -1.50201e+06 Fmax= 1.30033e+04, atom= 43072
Step= 65, Dmax= 1.5e-01 nm, Epot= -1.51026e+06 Fmax= 9.45520e+03, atom= 43072
Step= 66, Dmax= 1.8e-01 nm, Epot= -1.52076e+06 Fmax= 2.93103e+04, atom= 43072
Step= 67, Dmax= 2.2e-01 nm, Epot= -1.52717e+06 Fmax= 1.46174e+04, atom= 8665
Step= 68, Dmax= 2.7e-01 nm, Epot= -1.53761e+06 Fmax= 8.59420e+03, atom= 43072
Step= 69, Dmax= 3.2e-01 nm, Epot= -1.54272e+06 Fmax= 2.76372e+05, atom= 43072
Step= 71, Dmax= 1.9e-01 nm, Epot= -1.54942e+06 Fmax= 1.63669e+05, atom= 86652
Step= 72, Dmax= 2.3e-01 nm, Epot= -1.55500e+06 Fmax= 2.52620e+04, atom= 43072
Step= 73, Dmax= 2.8e-01 nm, Epot= -1.56080e+06 Fmax= 1.49968e+04, atom= 37288
Step= 75, Dmax= 1.7e-01 nm, Epot= -1.56569e+06 Fmax= 3.09219e+04, atom= 37516
Step= 77, Dmax= 9.9e-02 nm, Epot= -1.56856e+06 Fmax= 7.48726e+03, atom= 38353
Step= 78, Dmax= 1.2e-01 nm, Epot= -1.57447e+06 Fmax= 8.31583e+03, atom= 37297
Step= 79, Dmax= 1.4e-01 nm, Epot= -1.57797e+06 Fmax= 1.73976e+04, atom= 37516
Step= 80, Dmax= 1.7e-01 nm, Epot= -1.58257e+06 Fmax= 1.53833e+04, atom= 37516
Step= 81, Dmax= 2.1e-01 nm, Epot= -1.58510e+06 Fmax= 3.55585e+04, atom= 43222
Step= 82, Dmax= 2.5e-01 nm, Epot= -1.59115e+06 Fmax= 4.16977e+04, atom= 37516
Step= 84, Dmax= 1.5e-01 nm, Epot= -1.59270e+06 Fmax= 4.74577e+04, atom= 38353
Step= 85, Dmax= 1.8e-01 nm, Epot= -1.59428e+06 Fmax= 3.91391e+04, atom= 37297
Step= 87, Dmax= 1.1e-01 nm, Epot= -1.59618e+06 Fmax= 1.08481e+04, atom= 43228
Step= 88, Dmax= 1.3e-01 nm, Epot= -1.60037e+06 Fmax= 6.31705e+03, atom= 43084
Step= 89, Dmax= 1.5e-01 nm, Epot= -1.60617e+06 Fmax= 1.74501e+04, atom= 43084
Step= 90, Dmax= 1.8e-01 nm, Epot= -1.61032e+06 Fmax= 1.32463e+04, atom= 43084
Step= 92, Dmax= 1.1e-01 nm, Epot= -1.61361e+06 Fmax= 1.06311e+04, atom= 37342
Step= 93, Dmax= 1.3e-01 nm, Epot= -1.61677e+06 Fmax= 1.41706e+04, atom= 37342
Step= 94, Dmax= 1.6e-01 nm, Epot= -1.61927e+06 Fmax= 1.64830e+04, atom= 37342
Step= 95, Dmax= 1.9e-01 nm, Epot= -1.62109e+06 Fmax= 3.99218e+04, atom= 37342
Step= 97, Dmax= 1.1e-01 nm, Epot= -1.62487e+06 Fmax= 4.35303e+03, atom= 37344
Step= 98, Dmax= 1.4e-01 nm, Epot= -1.63037e+06 Fmax= 1.45321e+04, atom= 37342
Step= 99, Dmax= 1.6e-01 nm, Epot= -1.63284e+06 Fmax= 2.19512e+04, atom= 37654
Step= 100, Dmax= 2.0e-01 nm, Epot= -1.63400e+06 Fmax= 7.16513e+04, atom= 37342
Step= 101, Dmax= 2.4e-01 nm, Epot= -1.63748e+06 Fmax= 2.88877e+04, atom= 43213
Step= 103, Dmax= 1.4e-01 nm, Epot= -1.63950e+06 Fmax= 1.64369e+04, atom= 43213
Step= 104, Dmax= 1.7e-01 nm, Epot= -1.64329e+06 Fmax= 7.31695e+03, atom= 43213
Step= 105, Dmax= 2.1e-01 nm, Epot= -1.64539e+06 Fmax= 3.89980e+04, atom= 49297
Step= 107, Dmax= 1.2e-01 nm, Epot= -1.64988e+06 Fmax= 2.61257e+04, atom= 49297
Step= 108, Dmax= 1.5e-01 nm, Epot= -1.65178e+06 Fmax= 1.54480e+04, atom= 43717
Step= 109, Dmax= 1.8e-01 nm, Epot= -1.65484e+06 Fmax= 1.13275e+04, atom= 49297
Step= 111, Dmax= 1.1e-01 nm, Epot= -1.65755e+06 Fmax= 8.51706e+03, atom= 49297
Step= 112, Dmax= 1.3e-01 nm, Epot= -1.66090e+06 Fmax= 5.93986e+03, atom= 49297
Step= 113, Dmax= 1.5e-01 nm, Epot= -1.66473e+06 Fmax= 2.11430e+04, atom= 49297
Step= 114, Dmax= 1.8e-01 nm, Epot= -1.67090e+06 Fmax= 2.10983e+05, atom= 74057
Step= 119, Dmax= 1.4e-02 nm, Epot= -1.67268e+06 Fmax= 9.57021e+05, atom= 496681
Step= 123, Dmax= 2.1e-03 nm, Epot= -1.68715e+06 Fmax= 2.69819e+07, atom= 55505
Step= 126, Dmax= 6.2e-04 nm, Epot= -1.68933e+06 Fmax= 3.40027e+07, atom= 49668
Step= 128, Dmax= 3.7e-04 nm, Epot= -1.74204e+06 Fmax= 4.53874e+08, atom= 55505
Step= 131, Dmax= 1.1e-04 nm, Epot= -1.85324e+06 Fmax= 2.91012e+09, atom= 49668
Step= 134, Dmax= 3.3e-05 nm, Epot= -5.01184e+06 Fmax= 9.63139e+11, atom= 49668
Step= 139, Dmax= 2.5e-06 nm, Epot= -8.41932e+06 Fmax= 3.92665e+12, atom= 49668
Step= 141, Dmax= 1.5e-06 nm, Epot= -8.41932e+06 Fmax= 3.92665e+12, atom= 49668
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 142 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -8.4193190e+06
Maximum force = 3.9266461e+12 on atom 49668
Norm of force = 1.0642549e+10
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound.
Using 12 MPI processes
Using 1 OpenMP thread per MPI process
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 1000000
Step= 1, Dmax= 2.0e-02 nm, Epot= 1.90451e+08 Fmax= 2.44944e+06, atom= 175816
Step= 2, Dmax= 2.4e-02 nm, Epot= 6.43701e+07 Fmax= 1.52626e+06, atom= 196384
Step= 3, Dmax= 2.9e-02 nm, Epot= 5.91327e+07 Fmax= 8.43390e+05, atom= 192622
Step= 4, Dmax= 3.5e-02 nm, Epot= 5.39166e+07 Fmax= 5.20126e+05, atom= 192622
Step= 5, Dmax= 4.1e-02 nm, Epot= 4.96397e+07 Fmax= 3.50098e+05, atom= 192622
Step= 6, Dmax= 5.0e-02 nm, Epot= 4.61091e+07 Fmax= 1.15601e+05, atom= 231673
Step= 7, Dmax= 6.0e-02 nm, Epot= 3.95424e+07 Fmax= 1.56992e+05, atom= 128494
Step= 8, Dmax= 7.2e-02 nm, Epot= 3.57250e+07 Fmax= 5.88842e+04, atom= 128494
Step= 9, Dmax= 8.6e-02 nm, Epot= 2.62977e+07 Fmax= 1.02830e+05, atom= 181414
Step= 10, Dmax= 1.0e-01 nm, Epot= 2.17935e+07 Fmax= 2.99199e+04, atom= 258667
Step= 11, Dmax= 1.2e-01 nm, Epot= 1.82795e+07 Fmax= 2.14777e+07, atom= 262999
Step= 12, Dmax= 1.5e-01 nm, Epot= 1.01348e+07 Fmax= 5.17950e+05, atom= 174850
Step= 13, Dmax= 1.8e-01 nm, Epot= 1.00916e+07 Fmax= 1.87394e+06, atom= 180712
Step= 15, Dmax= 1.1e-01 nm, Epot= 9.40811e+06 Fmax= 3.43997e+05, atom= 180796
Step= 16, Dmax= 1.3e-01 nm, Epot= 8.85990e+06 Fmax= 3.60427e+04, atom= 180712
Step= 17, Dmax= 1.5e-01 nm, Epot= 4.59610e+06 Fmax= 4.47303e+04, atom= 158683
Step= 18, Dmax= 1.8e-01 nm, Epot= 2.57688e+06 Fmax= 3.06011e+05, atom= 175957
Step= 19, Dmax= 2.2e-01 nm, Epot= 2.41846e+06 Fmax= 1.22072e+07, atom= 158449
Step= 20, Dmax= 2.7e-01 nm, Epot= 2.19273e+06 Fmax= 1.65943e+05, atom= 180796
Step= 22, Dmax= 1.6e-01 nm, Epot= 1.86155e+06 Fmax= 4.61232e+05, atom= 163252
Step= 23, Dmax= 1.9e-01 nm, Epot= 1.71725e+06 Fmax= 2.74171e+04, atom= 157939
Step= 24, Dmax= 2.3e-01 nm, Epot= -1.23455e+05 Fmax= 4.00929e+05, atom= 43105
Step= 25, Dmax= 2.8e-01 nm, Epot= -2.08801e+05 Fmax= 8.84382e+05, atom= 43141
Step= 27, Dmax= 1.7e-01 nm, Epot= -2.22478e+05 Fmax= 7.37672e+05, atom= 43165
Step= 28, Dmax= 2.0e-01 nm, Epot= -2.29679e+05 Fmax= 1.99829e+06, atom= 38266
Step= 29, Dmax= 2.4e-01 nm, Epot= -2.78607e+05 Fmax= 7.14295e+04, atom= 38014
Step= 31, Dmax= 1.4e-01 nm, Epot= -4.46680e+05 Fmax= 2.06317e+05, atom= 43165
Step= 32, Dmax= 1.7e-01 nm, Epot= -5.06935e+05 Fmax= 1.14465e+05, atom= 37783
Step= 33, Dmax= 2.1e-01 nm, Epot= -6.11429e+05 Fmax= 1.76188e+05, atom= 39562
Step= 34, Dmax= 2.5e-01 nm, Epot= -6.94368e+05 Fmax= 4.90580e+04, atom= 37825
Step= 35, Dmax= 3.0e-01 nm, Epot= -8.97818e+05 Fmax= 1.83963e+06, atom= 37738
Step= 39, Dmax= 4.5e-02 nm, Epot= -9.23256e+05 Fmax= 8.12806e+05, atom= 43063
Step= 40, Dmax= 5.3e-02 nm, Epot= -9.41430e+05 Fmax= 2.21647e+05, atom= 37738
Step= 41, Dmax= 6.4e-02 nm, Epot= -9.54382e+05 Fmax= 8.79543e+04, atom= 43063
Step= 42, Dmax= 7.7e-02 nm, Epot= -9.79611e+05 Fmax= 1.58182e+04, atom= 43063
Step= 43, Dmax= 9.2e-02 nm, Epot= -1.10067e+06 Fmax= 1.20433e+04, atom= 37738
Step= 44, Dmax= 1.1e-01 nm, Epot= -1.20555e+06 Fmax= 1.43168e+04, atom= 43063
Step= 45, Dmax= 1.3e-01 nm, Epot= -1.25933e+06 Fmax= 9.65520e+03, atom= 43063
Step= 46, Dmax= 1.6e-01 nm, Epot= -1.31272e+06 Fmax= 4.06038e+04, atom= 43165
Step= 47, Dmax= 1.9e-01 nm, Epot= -1.32592e+06 Fmax= 4.51899e+04, atom= 38014
Step= 48, Dmax= 2.3e-01 nm, Epot= -1.34017e+06 Fmax= 1.32744e+04, atom= 37291
Step= 49, Dmax= 2.8e-01 nm, Epot= -1.37885e+06 Fmax= 4.62811e+04, atom= 37825
Step= 50, Dmax= 3.3e-01 nm, Epot= -1.39333e+06 Fmax= 3.04440e+04, atom= 37825
Step= 52, Dmax= 2.0e-01 nm, Epot= -1.40350e+06 Fmax= 3.62033e+04, atom= 43063
Step= 54, Dmax= 1.2e-01 nm, Epot= -1.40869e+06 Fmax= 2.70381e+04, atom= 43105
Step= 55, Dmax= 1.4e-01 nm, Epot= -1.41608e+06 Fmax= 2.07082e+04, atom= 37678
Step= 56, Dmax= 1.7e-01 nm, Epot= -1.42712e+06 Fmax= 1.02487e+04, atom= 37678
Step 57, time 0.057 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.340871, max 5.652700 (between atoms 59 and 60)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
59 60 168.5 0.1100 0.7318 0.1100
Back Off! I just backed up step57b_n0.pdb to ./#step57b_n0.pdb.1#
Back Off! I just backed up step57c_n0.pdb to ./#step57c_n0.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 58, Dmax= 1.0e-01 nm, Epot= -1.43984e+06 Fmax= 4.84458e+03, atom= 37288
Step= 59, Dmax= 1.2e-01 nm, Epot= -1.46546e+06 Fmax= 2.01342e+04, atom= 37288
Step= 60, Dmax= 1.5e-01 nm, Epot= -1.47391e+06 Fmax= 7.85587e+03, atom= 37288
Step= 61, Dmax= 1.8e-01 nm, Epot= -1.49067e+06 Fmax= 2.49859e+04, atom= 37288
Step= 62, Dmax= 2.1e-01 nm, Epot= -1.49833e+06 Fmax= 3.29761e+04, atom= 43072
Step= 64, Dmax= 1.3e-01 nm, Epot= -1.50201e+06 Fmax= 1.30033e+04, atom= 43072
Step= 65, Dmax= 1.5e-01 nm, Epot= -1.51026e+06 Fmax= 9.45520e+03, atom= 43072
Step= 66, Dmax= 1.8e-01 nm, Epot= -1.52076e+06 Fmax= 2.93103e+04, atom= 43072
Step= 67, Dmax= 2.2e-01 nm, Epot= -1.52717e+06 Fmax= 1.46174e+04, atom= 8665
Step= 68, Dmax= 2.7e-01 nm, Epot= -1.53761e+06 Fmax= 8.59420e+03, atom= 43072
Step= 69, Dmax= 3.2e-01 nm, Epot= -1.54272e+06 Fmax= 2.76372e+05, atom= 43072
Step= 71, Dmax= 1.9e-01 nm, Epot= -1.54942e+06 Fmax= 1.63669e+05, atom= 86652
Step= 72, Dmax= 2.3e-01 nm, Epot= -1.55500e+06 Fmax= 2.52620e+04, atom= 43072
Step= 73, Dmax= 2.8e-01 nm, Epot= -1.56080e+06 Fmax= 1.49968e+04, atom= 37288
Step= 75, Dmax= 1.7e-01 nm, Epot= -1.56569e+06 Fmax= 3.09219e+04, atom= 37516
Step= 77, Dmax= 9.9e-02 nm, Epot= -1.56856e+06 Fmax= 7.48726e+03, atom= 38353
Step= 78, Dmax= 1.2e-01 nm, Epot= -1.57447e+06 Fmax= 8.31583e+03, atom= 37297
Step= 79, Dmax= 1.4e-01 nm, Epot= -1.57797e+06 Fmax= 1.73976e+04, atom= 37516
Step= 80, Dmax= 1.7e-01 nm, Epot= -1.58257e+06 Fmax= 1.53833e+04, atom= 37516
Step= 81, Dmax= 2.1e-01 nm, Epot= -1.58510e+06 Fmax= 3.55585e+04, atom= 43222
Step= 82, Dmax= 2.5e-01 nm, Epot= -1.59115e+06 Fmax= 4.16977e+04, atom= 37516
Step= 84, Dmax= 1.5e-01 nm, Epot= -1.59270e+06 Fmax= 4.74577e+04, atom= 38353
Step= 85, Dmax= 1.8e-01 nm, Epot= -1.59428e+06 Fmax= 3.91391e+04, atom= 37297
Step= 87, Dmax= 1.1e-01 nm, Epot= -1.59618e+06 Fmax= 1.08481e+04, atom= 43228
Step= 88, Dmax= 1.3e-01 nm, Epot= -1.60037e+06 Fmax= 6.31705e+03, atom= 43084
Step= 89, Dmax= 1.5e-01 nm, Epot= -1.60617e+06 Fmax= 1.74501e+04, atom= 43084
Step= 90, Dmax= 1.8e-01 nm, Epot= -1.61032e+06 Fmax= 1.32463e+04, atom= 43084
Step= 92, Dmax= 1.1e-01 nm, Epot= -1.61361e+06 Fmax= 1.06311e+04, atom= 37342
Step= 93, Dmax= 1.3e-01 nm, Epot= -1.61677e+06 Fmax= 1.41706e+04, atom= 37342
Step= 94, Dmax= 1.6e-01 nm, Epot= -1.61927e+06 Fmax= 1.64830e+04, atom= 37342
Step= 95, Dmax= 1.9e-01 nm, Epot= -1.62109e+06 Fmax= 3.99218e+04, atom= 37342
Step= 97, Dmax= 1.1e-01 nm, Epot= -1.62487e+06 Fmax= 4.35303e+03, atom= 37344
Step= 98, Dmax= 1.4e-01 nm, Epot= -1.63037e+06 Fmax= 1.45321e+04, atom= 37342
Step= 99, Dmax= 1.6e-01 nm, Epot= -1.63284e+06 Fmax= 2.19512e+04, atom= 37654
Step= 100, Dmax= 2.0e-01 nm, Epot= -1.63400e+06 Fmax= 7.16513e+04, atom= 37342
Step= 101, Dmax= 2.4e-01 nm, Epot= -1.63748e+06 Fmax= 2.88877e+04, atom= 43213
Step= 103, Dmax= 1.4e-01 nm, Epot= -1.63950e+06 Fmax= 1.64369e+04, atom= 43213
Step= 104, Dmax= 1.7e-01 nm, Epot= -1.64329e+06 Fmax= 7.31695e+03, atom= 43213
Step= 105, Dmax= 2.1e-01 nm, Epot= -1.64539e+06 Fmax= 3.89980e+04, atom= 49297
Step= 107, Dmax= 1.2e-01 nm, Epot= -1.64988e+06 Fmax= 2.61257e+04, atom= 49297
Step= 108, Dmax= 1.5e-01 nm, Epot= -1.65178e+06 Fmax= 1.54480e+04, atom= 43717
Step= 109, Dmax= 1.8e-01 nm, Epot= -1.65484e+06 Fmax= 1.13275e+04, atom= 49297
Step= 111, Dmax= 1.1e-01 nm, Epot= -1.65755e+06 Fmax= 8.51706e+03, atom= 49297
Step= 112, Dmax= 1.3e-01 nm, Epot= -1.66090e+06 Fmax= 5.93986e+03, atom= 49297
Step= 113, Dmax= 1.5e-01 nm, Epot= -1.66473e+06 Fmax= 2.11430e+04, atom= 49297
Step= 114, Dmax= 1.8e-01 nm, Epot= -1.67090e+06 Fmax= 2.10983e+05, atom= 74057
Step= 119, Dmax= 1.4e-02 nm, Epot= -1.67268e+06 Fmax= 9.57021e+05, atom= 496681
Step= 123, Dmax= 2.1e-03 nm, Epot= -1.68715e+06 Fmax= 2.69819e+07, atom= 55505
Step= 126, Dmax= 6.2e-04 nm, Epot= -1.68933e+06 Fmax= 3.40027e+07, atom= 49668
Step= 128, Dmax= 3.7e-04 nm, Epot= -1.74204e+06 Fmax= 4.53874e+08, atom= 55505
Step= 131, Dmax= 1.1e-04 nm, Epot= -1.85324e+06 Fmax= 2.91012e+09, atom= 49668
Step= 134, Dmax= 3.3e-05 nm, Epot= -5.01184e+06 Fmax= 9.63139e+11, atom= 49668
Step= 139, Dmax= 2.5e-06 nm, Epot= -8.41932e+06 Fmax= 3.92665e+12, atom= 49668
Step= 141, Dmax= 1.5e-06 nm, Epot= -8.41932e+06 Fmax= 3.92665e+12, atom= 49668
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 142 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -8.4193190e+06
Maximum force = 3.9266461e+12 on atom 49668
Norm of force = 1.0642549e+10
8. I changed my PW stiff bonds to constraints again:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;;;;;; POLARIZABLE WATER
[ moleculetype ]
; molname nrexcl
PW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 PW W 1 0
2 D 1 PW WP 1 0.457
3 D 1 PW WM 1 -0.457
[constraints]
; i j funct length
1 2 1 0.14
1 3 1 0.14
; for minimization purposes constraints might be replaced by stiff bonds:
;
;[bonds]
; i j funct length force const.
; 1 2 1 0.14 50000
; 1 3 1 0.14 50000
[angles]
; i j k funct angle fc
2 1 3 2 0.0 4.20
[exclusions]
1 2 3
2 3
[ moleculetype ]
; molname nrexcl
PW 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 PW W 1 0
2 D 1 PW WP 1 0.457
3 D 1 PW WM 1 -0.457
[constraints]
; i j funct length
1 2 1 0.14
1 3 1 0.14
; for minimization purposes constraints might be replaced by stiff bonds:
;
;[bonds]
; i j funct length force const.
; 1 2 1 0.14 50000
; 1 3 1 0.14 50000
[angles]
; i j k funct angle fc
2 1 3 2 0.0 4.20
[exclusions]
1 2 3
2 3
and tried to run my EQ with 10fs first.
gmx grompp -f EQ.mdp -c EM.gro -p topol.top -o EQ10.tpr
mpirun -np 12 -host node02 mdrun_mpi -v -deffnm EQ10
This is my EQ.mdp:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
; MARTINI NVT mdp
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.01
nsteps = 10000
comm-mode = Linear
nstcomm = 100
comm-grps =
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
tc-grps = Protein Non-Protein
tau_t = 1.0 1.0
ref_t = 300 300
; pressure coupling
pcoupl = no
refcoord-scaling = COM
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen-seed = -1
; OPTIONS FOR BONDS
constraints = none
constraint_algorithm = lincs
continuation = no
lincs_order = 8
lincs_iter = 2
lincs-warnangle = 90
morse = no
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.01
nsteps = 10000
comm-mode = Linear
nstcomm = 100
comm-grps =
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.005
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.1
epsilon-r = 2.5
epsilon-rf = 0
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw-switch = 0
rvdw = 1.1
DispCorr = no
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
tc-grps = Protein Non-Protein
tau_t = 1.0 1.0
ref_t = 300 300
; pressure coupling
pcoupl = no
refcoord-scaling = COM
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen-seed = -1
; OPTIONS FOR BONDS
constraints = none
constraint_algorithm = lincs
continuation = no
lincs_order = 8
lincs_iter = 2
lincs-warnangle = 90
morse = no
However, my system crashes with the following error:
Warning: Spoiler!
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[ Click to hide ]
Reading file EQ10.tpr, VERSION 5.0.7 (single precision)
Changing nstlist from 20 to 25, rlist from 1.1 to 1.114
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound.
Using 12 MPI processes
Using 1 OpenMP thread per MPI process
starting mdrun 'Martini system from 2b97_A.pdb'
10000 steps, 100.0 ps.
step 0
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000417, max 0.046662 (between atoms 74058 and 74056)
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009630, max 0.790648 (between atoms 49667 and 49666)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021116, max 1.872200 (between atoms 181992 and 181990)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
29795 29794 105.5 0.1400 0.1736 0.1400
25761 25759 109.9 0.1400 0.1822 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55506 55504 125.2 0.1400 0.2431 0.1400
49667 49666 123.9 0.1400 0.2507 0.1400
74058 74056 91.0 0.1400 0.1335 0.1400
68147 68146 93.4 0.1400 0.1383 0.1400
186617 186616 111.3 0.1400 0.3858 0.1400
181992 181990 110.4 0.1400 0.4021 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052642, max 4.574347 (between atoms 181758 and 181756)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.293767, max 16.232697 (between atoms 55391 and 55390)
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.860547, max 76.945740 (between atoms 181992 and 181990)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
25760 25759 95.5 0.1596 0.1501 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55391 55390 93.4 0.1400 2.4126 0.1400
55392 55390 93.5 0.1400 2.3108 0.1400
186398 186397 103.9 0.1400 0.5837 0.1400
186399 186397 101.9 0.1400 0.6817 0.1400
186617 186616 105.7 0.3858 0.5172 0.1400
55505 55504 96.5 0.1849 1.2305 0.1400
186618 186616 109.1 0.1956 0.4296 0.1400
181991 181990 90.8 0.1921 10.7704 0.1400
181992 181990 90.8 0.4021 10.9124 0.1400
181757 181756 100.3 0.1400 0.7798 0.1400
181758 181756 100.3 0.1400 0.7804 0.1400
55506 55504 96.7 0.2431 1.1894 0.1400
49667 49666 93.4 0.2507 2.2947 0.1400
49668 49666 93.3 0.1880 2.3625 0.1400
55280 55279 95.3 0.1400 1.5244 0.1400
55281 55279 95.6 0.1400 1.4251 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007304, max 0.790561 (between atoms 181757 and 181756)
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 18.884724, max 1340.137451 (between atoms 181272 and 181270)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
25752 25750 107.1 0.1400 0.1924 0.1400
29795 29794 100.5 0.1399 0.1631 0.1400
29796 29794 103.9 0.1400 0.1790 0.1400
25760 25759 114.1 0.1501 0.1880 0.1400
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.121164, max 7.090692 (between atoms 56141 and 56140)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55391 55390 113.5 2.4126 0.3667 0.1400
55392 55390 102.3 2.3108 0.6874 0.1400
55505 55504 112.8 1.2305 0.3733 0.1400
55506 55504 120.5 1.1894 0.2859 0.1400
49668 49666 117.6 2.3625 0.3208 0.1400
50432 50431 120.3 0.1400 0.2782 0.1400
50433 50431 123.9 0.1400 0.2518 0.1400
55280 55279 97.5 1.5244 1.1017 0.1400
55281 55279 97.5 1.4251 1.0998 0.1400
56141 56140 97.1 0.1400 1.1327 0.1400
56142 56140 97.2 0.1400 1.1322 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
141476 141475 90.8 0.1400 12.2581 0.1400
141477 141475 90.8 0.1400 12.2106 0.1400
141989 141988 119.1 0.1400 0.2885 0.1400
141990 141988 121.4 0.1400 0.2695 0.1400
186398 186397 90.4 0.5837 19.1331 0.1400
186399 186397 90.4 0.6817 19.8611 0.1400
181757 181756 124.6 0.7798 0.2507 0.1400
181758 181756 104.6 0.7804 0.1994 0.1400
181271 181270 90.0 0.1400 179.9774 0.1400
186617 186616 90.1 0.5172 139.9016 0.1400
186618 186616 90.1 0.4296 150.2379 0.1400
181991 181990 95.2 10.7704 1.9040 0.1400
181992 181990 97.9 10.9124 1.2572 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Program mdrun_mpi, VERSION 5.0.7
Source code file: /home/disk/gromacs/gromacs-5.0.7/src/gromacs/mdlib/pme.c, line: 754
Fatal error:
1 particles communicated to PME rank 8 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Error on rank 8, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 8 out of 12
gcq#68: "What's Your Definition Of Dirty ?" (G. Michael)
MPI_ABORT was invoked on rank 8 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpirun has exited due to process rank 8 with PID 43654 on
node node02 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Changing nstlist from 20 to 25, rlist from 1.1 to 1.114
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound.
Using 12 MPI processes
Using 1 OpenMP thread per MPI process
starting mdrun 'Martini system from 2b97_A.pdb'
10000 steps, 100.0 ps.
step 0
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000417, max 0.046662 (between atoms 74058 and 74056)
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009630, max 0.790648 (between atoms 49667 and 49666)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021116, max 1.872200 (between atoms 181992 and 181990)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
29795 29794 105.5 0.1400 0.1736 0.1400
25761 25759 109.9 0.1400 0.1822 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55506 55504 125.2 0.1400 0.2431 0.1400
49667 49666 123.9 0.1400 0.2507 0.1400
74058 74056 91.0 0.1400 0.1335 0.1400
68147 68146 93.4 0.1400 0.1383 0.1400
186617 186616 111.3 0.1400 0.3858 0.1400
181992 181990 110.4 0.1400 0.4021 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052642, max 4.574347 (between atoms 181758 and 181756)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.293767, max 16.232697 (between atoms 55391 and 55390)
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.860547, max 76.945740 (between atoms 181992 and 181990)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
25760 25759 95.5 0.1596 0.1501 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55391 55390 93.4 0.1400 2.4126 0.1400
55392 55390 93.5 0.1400 2.3108 0.1400
186398 186397 103.9 0.1400 0.5837 0.1400
186399 186397 101.9 0.1400 0.6817 0.1400
186617 186616 105.7 0.3858 0.5172 0.1400
55505 55504 96.5 0.1849 1.2305 0.1400
186618 186616 109.1 0.1956 0.4296 0.1400
181991 181990 90.8 0.1921 10.7704 0.1400
181992 181990 90.8 0.4021 10.9124 0.1400
181757 181756 100.3 0.1400 0.7798 0.1400
181758 181756 100.3 0.1400 0.7804 0.1400
55506 55504 96.7 0.2431 1.1894 0.1400
49667 49666 93.4 0.2507 2.2947 0.1400
49668 49666 93.3 0.1880 2.3625 0.1400
55280 55279 95.3 0.1400 1.5244 0.1400
55281 55279 95.6 0.1400 1.4251 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007304, max 0.790561 (between atoms 181757 and 181756)
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 18.884724, max 1340.137451 (between atoms 181272 and 181270)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
25752 25750 107.1 0.1400 0.1924 0.1400
29795 29794 100.5 0.1399 0.1631 0.1400
29796 29794 103.9 0.1400 0.1790 0.1400
25760 25759 114.1 0.1501 0.1880 0.1400
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.121164, max 7.090692 (between atoms 56141 and 56140)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
55391 55390 113.5 2.4126 0.3667 0.1400
55392 55390 102.3 2.3108 0.6874 0.1400
55505 55504 112.8 1.2305 0.3733 0.1400
55506 55504 120.5 1.1894 0.2859 0.1400
49668 49666 117.6 2.3625 0.3208 0.1400
50432 50431 120.3 0.1400 0.2782 0.1400
50433 50431 123.9 0.1400 0.2518 0.1400
55280 55279 97.5 1.5244 1.1017 0.1400
55281 55279 97.5 1.4251 1.0998 0.1400
56141 56140 97.1 0.1400 1.1327 0.1400
56142 56140 97.2 0.1400 1.1322 0.1400
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
141476 141475 90.8 0.1400 12.2581 0.1400
141477 141475 90.8 0.1400 12.2106 0.1400
141989 141988 119.1 0.1400 0.2885 0.1400
141990 141988 121.4 0.1400 0.2695 0.1400
186398 186397 90.4 0.5837 19.1331 0.1400
186399 186397 90.4 0.6817 19.8611 0.1400
181757 181756 124.6 0.7798 0.2507 0.1400
181758 181756 104.6 0.7804 0.1994 0.1400
181271 181270 90.0 0.1400 179.9774 0.1400
186617 186616 90.1 0.5172 139.9016 0.1400
186618 186616 90.1 0.4296 150.2379 0.1400
181991 181990 95.2 10.7704 1.9040 0.1400
181992 181990 97.9 10.9124 1.2572 0.1400
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Program mdrun_mpi, VERSION 5.0.7
Source code file: /home/disk/gromacs/gromacs-5.0.7/src/gromacs/mdlib/pme.c, line: 754
Fatal error:
1 particles communicated to PME rank 8 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Error on rank 8, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 8 out of 12
gcq#68: "What's Your Definition Of Dirty ?" (G. Michael)
MPI_ABORT was invoked on rank 8 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpirun has exited due to process rank 8 with PID 43654 on
node node02 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Now, when I checked these LINCS erred molecules from EM.gro, I noticed that the water molecules were bent during EM
Does anyone know why this is happening? I looked up various things but I just can't seem to find out the solution.
Oh FYI, here are my topology and Protein_A.itp files:
topol.top
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
#include "martini_v2.2refP.itp"
#include "martini_v2.2p_aminoacids.itp"
#include "martini_v2.0_ions.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from 2b97_A.pdb
[ molecules ]
; name number
Protein_A 48
PW 88017
#include "martini_v2.2p_aminoacids.itp"
#include "martini_v2.0_ions.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from 2b97_A.pdb
[ molecules ]
; name number
Protein_A 48
PW 88017
Protein_A.itp
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
; MARTINI (martini22p) Coarse Grained topology file for "Protein_A"
; Created by py version 2.6
; Using the following options: -f Protein.pdb -ss Protein.dssp -p backbone -ff martini22p -o topol.top -x Protein_CG.pdb -v
; Sequence:
; AVCPTGLFSNPLCCATNVLDLIGVDCKTPTIAVDTGAIFQAHCASKGSKPLCCVAPVADQALLCQKAIGT
; Secondary Structure:
; CCSCSSTTCEEEEEEEEETTTEEEEEECCSSCCCS1111HH2222TTCEEEEESCSSCEEEEEEEECTTC
[ moleculetype ]
; Name Exclusions
Protein_A 1
[ atoms ]
1 Qd 1 ALA BB 1 1.0000 ; C
2 P5 2 VAL BB 2 0.0000 ; C
3 C2 2 VAL SC1 3 0.0000 ; C
4 P5 3 CYS BB 4 0.0000 ; S
5 C5 3 CYS SC1 5 0.0000 ; S
6 P4 4 PRO BB 6 0.0000 ; C
7 C3 4 PRO SC1 7 0.0000 ; C
8 P5 5 THR BB 8 0.0000 ; S
9 N0 5 THR SC1 9 0.0000 0.0000 ; S
10 D 5 THR SCP 10 0.3600 36.0000 ; S
11 D 5 THR SCN 11 -0.3600 36.0000 ; S
12 P5 6 GLY BB 12 0.0000 ; S
13 Nda 7 LEU BB 13 0.0000 ; T
14 C1 7 LEU SC1 14 0.0000 ; T
15 Nda 8 PHE BB 15 0.0000 ; T
16 SC5 8 PHE SC1 16 0.0000 ; T
17 SC5 8 PHE SC2 17 0.0000 ; T
18 SC5 8 PHE SC3 18 0.0000 ; T
19 P5 9 SER BB 19 0.0000 ; C
20 N0 9 SER SC1 20 0.0000 0.0000 ; C
21 D 9 SER SCP 21 0.4000 36.0000 ; C
22 D 9 SER SCN 22 -0.4000 36.0000 ; C
23 Nda 10 ASN BB 23 0.0000 ; E
24 Nda 10 ASN SC1 24 0.0000 0.0000 ; E
25 D 10 ASN SCP 25 0.4600 36.0000 ; E
26 D 10 ASN SCN 26 -0.4600 36.0000 ; E
27 N0 11 PRO BB 27 0.0000 ; E
28 C3 11 PRO SC1 28 0.0000 ; E
29 Nda 12 LEU BB 29 0.0000 ; E
30 C1 12 LEU SC1 30 0.0000 ; E
31 Nda 13 CYS BB 31 0.0000 ; E
32 C5 13 CYS SC1 32 0.0000 ; E
33 Nda 14 CYS BB 33 0.0000 ; E
34 C5 14 CYS SC1 34 0.0000 ; E
35 N0 15 ALA BB 35 0.0000 ; E
36 Nda 16 THR BB 36 0.0000 ; E
37 N0 16 THR SC1 37 0.0000 0.0000 ; E
38 D 16 THR SCP 38 0.3600 36.0000 ; E
39 D 16 THR SCN 39 -0.3600 36.0000 ; E
40 Nda 17 ASN BB 40 0.0000 ; E
41 Nda 17 ASN SC1 41 0.0000 0.0000 ; E
42 D 17 ASN SCP 42 0.4600 36.0000 ; E
43 D 17 ASN SCN 43 -0.4600 36.0000 ; E
44 Nda 18 VAL BB 44 0.0000 ; E
45 C2 18 VAL SC1 45 0.0000 ; E
46 Nda 19 LEU BB 46 0.0000 ; T
47 C1 19 LEU SC1 47 0.0000 ; T
48 Nda 20 ASP BB 48 0.0000 ; T
49 Qa 20 ASP SC1 49 0.0000 36.0000 ; T
50 D 20 ASP SCN 50 -1.0000 36.0000 ; T
51 Nda 21 LEU BB 51 0.0000 ; T
52 C1 21 LEU SC1 52 0.0000 ; T
53 Nda 22 ILE BB 53 0.0000 ; E
54 C1 22 ILE SC1 54 0.0000 ; E
55 Nda 23 GLY BB 55 0.0000 ; E
56 Nda 24 VAL BB 56 0.0000 ; E
57 C2 24 VAL SC1 57 0.0000 ; E
58 Nda 25 ASP BB 58 0.0000 ; E
59 Qa 25 ASP SC1 59 0.0000 36.0000 ; E
60 D 25 ASP SCN 60 -1.0000 36.0000 ; E
61 Nda 26 CYS BB 61 0.0000 ; E
62 C5 26 CYS SC1 62 0.0000 ; E
63 Nda 27 LYS BB 63 0.0000 ; E
64 C3 27 LYS SC1 64 0.0000 72.0000 ; E
65 Qd 27 LYS SC2 65 0.0000 36.0000 ; E
66 D 27 LYS SCP 66 1.0000 36.0000 ; E
67 P5 28 THR BB 67 0.0000 ; C
68 N0 28 THR SC1 68 0.0000 0.0000 ; C
69 D 28 THR SCP 69 0.3600 36.0000 ; C
70 D 28 THR SCN 70 -0.3600 36.0000 ; C
71 P4 29 PRO BB 71 0.0000 ; C
72 C3 29 PRO SC1 72 0.0000 ; C
73 P5 30 THR BB 73 0.0000 ; S
74 N0 30 THR SC1 74 0.0000 0.0000 ; S
75 D 30 THR SCP 75 0.3600 36.0000 ; S
76 D 30 THR SCN 76 -0.3600 36.0000 ; S
77 P5 31 ILE BB 77 0.0000 ; S
78 C1 31 ILE SC1 78 0.0000 ; S
79 P4 32 ALA BB 79 0.0000 ; C
80 P5 33 VAL BB 80 0.0000 ; C
81 C2 33 VAL SC1 81 0.0000 ; C
82 P5 34 ASP BB 82 0.0000 ; C
83 Qa 34 ASP SC1 83 0.0000 36.0000 ; C
84 D 34 ASP SCN 84 -1.0000 36.0000 ; C
85 P5 35 THR BB 85 0.0000 ; S
86 N0 35 THR SC1 86 0.0000 0.0000 ; S
87 D 35 THR SCP 87 0.3600 36.0000 ; S
88 D 35 THR SCN 88 -0.3600 36.0000 ; S
89 Nd 36 GLY BB 89 0.0000 ; 1
90 N0 37 ALA BB 90 0.0000 ; 1
91 Nd 38 ILE BB 91 0.0000 ; 1
92 C1 38 ILE SC1 92 0.0000 ; 1
93 Nd 39 PHE BB 93 0.0000 ; 1
94 SC5 39 PHE SC1 94 0.0000 ; 1
95 SC5 39 PHE SC2 95 0.0000 ; 1
96 SC5 39 PHE SC3 96 0.0000 ; 1
97 N0 40 GLN BB 97 0.0000 ; H
98 Nda 40 GLN SC1 98 0.0000 0.0000 ; H
99 D 40 GLN SCP 99 0.4200 36.0000 ; H
100 D 40 GLN SCN 100 -0.4200 36.0000 ; H
101 C5 41 ALA BB 101 0.0000 ; H
102 Na 42 HIS BB 102 0.0000 ; 2
103 SC4 42 HIS SC1 103 0.0000 ; 2
104 SP1 42 HIS SC2 104 0.0000 ; 2
105 SP1 42 HIS SC3 105 0.0000 ; 2
106 Na 43 CYS BB 106 0.0000 ; 2
107 C5 43 CYS SC1 107 0.0000 ; 2
108 N0 44 ALA BB 108 0.0000 ; 2
109 Na 45 SER BB 109 0.0000 ; 2
110 N0 45 SER SC1 110 0.0000 0.0000 ; 2
111 D 45 SER SCP 111 0.4000 36.0000 ; 2
112 D 45 SER SCN 112 -0.4000 36.0000 ; 2
113 Nda 46 LYS BB 113 0.0000 ; T
114 C3 46 LYS SC1 114 0.0000 72.0000 ; T
115 Qd 46 LYS SC2 115 0.0000 36.0000 ; T
116 D 46 LYS SCP 116 1.0000 36.0000 ; T
117 Nda 47 GLY BB 117 0.0000 ; T
118 P5 48 SER BB 118 0.0000 ; C
119 N0 48 SER SC1 119 0.0000 0.0000 ; C
120 D 48 SER SCP 120 0.4000 36.0000 ; C
121 D 48 SER SCN 121 -0.4000 36.0000 ; C
122 Nda 49 LYS BB 122 0.0000 ; E
123 C3 49 LYS SC1 123 0.0000 72.0000 ; E
124 Qd 49 LYS SC2 124 0.0000 36.0000 ; E
125 D 49 LYS SCP 125 1.0000 36.0000 ; E
126 N0 50 PRO BB 126 0.0000 ; E
127 C3 50 PRO SC1 127 0.0000 ; E
128 Nda 51 LEU BB 128 0.0000 ; E
129 C1 51 LEU SC1 129 0.0000 ; E
130 Nda 52 CYS BB 130 0.0000 ; E
131 C5 52 CYS SC1 131 0.0000 ; E
132 Nda 53 CYS BB 132 0.0000 ; E
133 C5 53 CYS SC1 133 0.0000 ; E
134 P5 54 VAL BB 134 0.0000 ; S
135 C2 54 VAL SC1 135 0.0000 ; S
136 P4 55 ALA BB 136 0.0000 ; C
137 P4 56 PRO BB 137 0.0000 ; S
138 C3 56 PRO SC1 138 0.0000 ; S
139 P5 57 VAL BB 139 0.0000 ; S
140 C2 57 VAL SC1 140 0.0000 ; S
141 P4 58 ALA BB 141 0.0000 ; C
142 Nda 59 ASP BB 142 0.0000 ; E
143 Qa 59 ASP SC1 143 0.0000 36.0000 ; E
144 D 59 ASP SCN 144 -1.0000 36.0000 ; E
145 Nda 60 GLN BB 145 0.0000 ; E
146 Nda 60 GLN SC1 146 0.0000 0.0000 ; E
147 D 60 GLN SCP 147 0.4200 36.0000 ; E
148 D 60 GLN SCN 148 -0.4200 36.0000 ; E
149 N0 61 ALA BB 149 0.0000 ; E
150 Nda 62 LEU BB 150 0.0000 ; E
151 C1 62 LEU SC1 151 0.0000 ; E
152 Nda 63 LEU BB 152 0.0000 ; E
153 C1 63 LEU SC1 153 0.0000 ; E
154 Nda 64 CYS BB 154 0.0000 ; E
155 C5 64 CYS SC1 155 0.0000 ; E
156 Nda 65 GLN BB 156 0.0000 ; E
157 Nda 65 GLN SC1 157 0.0000 0.0000 ; E
158 D 65 GLN SCP 158 0.4200 36.0000 ; E
159 D 65 GLN SCN 159 -0.4200 36.0000 ; E
160 Nda 66 LYS BB 160 0.0000 ; E
161 C3 66 LYS SC1 161 0.0000 72.0000 ; E
162 Qd 66 LYS SC2 162 0.0000 36.0000 ; E
163 D 66 LYS SCP 163 1.0000 36.0000 ; E
164 P4 67 ALA BB 164 0.0000 ; C
165 Nda 68 ILE BB 165 0.0000 ; T
166 C1 68 ILE SC1 166 0.0000 ; T
167 Nda 69 GLY BB 167 0.0000 ; T
168 Qa 70 THR BB 168 -1.0000 ; C
169 N0 70 THR SC1 169 0.0000 0.0000 ; C
170 D 70 THR SCP 170 0.3600 36.0000 ; C
171 D 70 THR SCN 171 -0.3600 36.0000 ; C
[ virtual_sites2 ]
9 10 11 1 0.50000 ; THR
20 21 22 1 0.50000 ; SER
24 25 26 1 0.50000 ; ASN
37 38 39 1 0.50000 ; THR
41 42 43 1 0.50000 ; ASN
68 69 70 1 0.50000 ; THR
74 75 76 1 0.50000 ; THR
86 87 88 1 0.50000 ; THR
98 99 100 1 0.50000 ; GLN
110 111 112 1 0.50000 ; SER
119 120 121 1 0.50000 ; SER
146 147 148 1 0.50000 ; GLN
157 158 159 1 0.50000 ; GLN
169 170 171 1 0.50000 ; THR
[ exclusions ]
168 170 ; THR(70)
168 171 ; THR(70)
[ bonds ]
; Backbone bonds
1 2 1 0.35000 1250 ; ALA(C)-VAL(C)
2 4 1 0.35000 1250 ; VAL(C)-CYS(S)
4 6 1 0.35000 1250 ; CYS(S)-PRO(C)
6 8 1 0.35000 1250 ; PRO(C)-THR(S)
8 12 1 0.35000 1250 ; THR(S)-GLY(S)
12 13 1 0.35000 1250 ; GLY(S)-LEU(T)
13 15 1 0.35000 1250 ; LEU(T)-PHE(T)
15 19 1 0.35000 1250 ; PHE(T)-SER(C)
19 23 1 0.35000 1250 ; SER(C)-ASN(E)
23 27 1 0.35000 1250 ; ASN(E)-PRO(E)
27 29 1 0.35000 1250 ; PRO(E)-LEU(E)
29 31 1 0.35000 1250 ; LEU(E)-CYS(E)
31 33 1 0.35000 1250 ; CYS(E)-CYS(E)
33 35 1 0.35000 1250 ; CYS(E)-ALA(E)
35 36 1 0.35000 1250 ; ALA(E)-THR(E)
36 40 1 0.35000 1250 ; THR(E)-ASN(E)
40 44 1 0.35000 1250 ; ASN(E)-VAL(E)
44 46 1 0.35000 1250 ; VAL(E)-LEU(T)
46 48 1 0.35000 1250 ; LEU(T)-ASP(T)
48 51 1 0.35000 1250 ; ASP(T)-LEU(T)
51 53 1 0.35000 1250 ; LEU(T)-ILE(E)
53 55 1 0.35000 1250 ; ILE(E)-GLY(E)
55 56 1 0.35000 1250 ; GLY(E)-VAL(E)
56 58 1 0.35000 1250 ; VAL(E)-ASP(E)
58 61 1 0.35000 1250 ; ASP(E)-CYS(E)
61 63 1 0.35000 1250 ; CYS(E)-LYS(E)
63 67 1 0.35000 1250 ; LYS(E)-THR(C)
67 71 1 0.35000 1250 ; THR(C)-PRO(C)
71 73 1 0.35000 1250 ; PRO(C)-THR(S)
73 77 1 0.35000 1250 ; THR(S)-ILE(S)
77 79 1 0.35000 1250 ; ILE(S)-ALA(C)
79 80 1 0.35000 1250 ; ALA(C)-VAL(C)
80 82 1 0.35000 1250 ; VAL(C)-ASP(C)
82 85 1 0.35000 1250 ; ASP(C)-THR(S)
113 117 1 0.35000 1250 ; LYS(T)-GLY(T)
117 118 1 0.35000 1250 ; GLY(T)-SER(C)
118 122 1 0.35000 1250 ; SER(C)-LYS(E)
122 126 1 0.35000 1250 ; LYS(E)-PRO(E)
126 128 1 0.35000 1250 ; PRO(E)-LEU(E)
128 130 1 0.35000 1250 ; LEU(E)-CYS(E)
130 132 1 0.35000 1250 ; CYS(E)-CYS(E)
132 134 1 0.35000 1250 ; CYS(E)-VAL(S)
134 136 1 0.35000 1250 ; VAL(S)-ALA(C)
136 137 1 0.35000 1250 ; ALA(C)-PRO(S)
137 139 1 0.35000 1250 ; PRO(S)-VAL(S)
139 141 1 0.35000 1250 ; VAL(S)-ALA(C)
141 142 1 0.35000 1250 ; ALA(C)-ASP(E)
142 145 1 0.35000 1250 ; ASP(E)-GLN(E)
145 149 1 0.35000 1250 ; GLN(E)-ALA(E)
149 150 1 0.35000 1250 ; ALA(E)-LEU(E)
150 152 1 0.35000 1250 ; LEU(E)-LEU(E)
152 154 1 0.35000 1250 ; LEU(E)-CYS(E)
154 156 1 0.35000 1250 ; CYS(E)-GLN(E)
156 160 1 0.35000 1250 ; GLN(E)-LYS(E)
160 164 1 0.35000 1250 ; LYS(E)-ALA(C)
164 165 1 0.35000 1250 ; ALA(C)-ILE(T)
165 167 1 0.35000 1250 ; ILE(T)-GLY(T)
167 168 1 0.35000 1250 ; GLY(T)-THR(C)
; Sidechain bonds
4 5 1 0.31000 7500 ; CYS
6 7 1 0.30000 7500 ; PRO
8 9 1 0.26000 9000 ; THR
13 14 1 0.33000 7500 ; LEU
15 16 1 0.31000 7500 ; PHE
19 20 1 0.25000 7500 ; SER
23 24 1 0.32000 5000 ; ASN
27 28 1 0.30000 7500 ; PRO
29 30 1 0.33000 7500 ; LEU
31 32 1 0.31000 7500 ; CYS
33 34 1 0.31000 7500 ; CYS
36 37 1 0.26000 9000 ; THR
40 41 1 0.32000 5000 ; ASN
46 47 1 0.33000 7500 ; LEU
48 49 1 0.32000 7500 ; ASP
51 52 1 0.33000 7500 ; LEU
58 59 1 0.32000 7500 ; ASP
61 62 1 0.31000 7500 ; CYS
63 64 1 0.33000 5000 ; LYS
64 65 1 0.28000 5000 ; LYS
67 68 1 0.26000 9000 ; THR
71 72 1 0.30000 7500 ; PRO
73 74 1 0.26000 9000 ; THR
82 83 1 0.32000 7500 ; ASP
85 86 1 0.26000 9000 ; THR
93 94 1 0.31000 7500 ; PHE
97 98 1 0.40000 5000 ; GLN
102 103 1 0.32000 7500 ; HIS
106 107 1 0.31000 7500 ; CYS
109 110 1 0.25000 7500 ; SER
113 114 1 0.33000 5000 ; LYS
114 115 1 0.28000 5000 ; LYS
118 119 1 0.25000 7500 ; SER
122 123 1 0.33000 5000 ; LYS
123 124 1 0.28000 5000 ; LYS
126 127 1 0.30000 7500 ; PRO
128 129 1 0.33000 7500 ; LEU
130 131 1 0.31000 7500 ; CYS
132 133 1 0.31000 7500 ; CYS
137 138 1 0.30000 7500 ; PRO
142 143 1 0.32000 7500 ; ASP
145 146 1 0.40000 5000 ; GLN
150 151 1 0.33000 7500 ; LEU
152 153 1 0.33000 7500 ; LEU
154 155 1 0.31000 7500 ; CYS
156 157 1 0.40000 5000 ; GLN
160 161 1 0.33000 5000 ; LYS
161 162 1 0.28000 5000 ; LYS
168 169 1 0.26000 9000 ; THR
; Short elastic bonds for extended regions
23 29 1 0.64000 2500 ; ASN(23)-LEU(29) 1-3
27 31 1 0.64000 2500 ; PRO(27)-CYS(31) 2-4
29 33 1 0.64000 2500 ; LEU(29)-CYS(33) 2-4
31 35 1 0.64000 2500 ; CYS(31)-ALA(35) 2-4
33 36 1 0.64000 2500 ; CYS(33)-THR(36) 2-4
35 40 1 0.64000 2500 ; ALA(35)-ASN(40) 2-4
36 44 1 0.64000 2500 ; THR(36)-VAL(44) 2-4
53 56 1 0.64000 2500 ; ILE(53)-VAL(56) 1-3
55 58 1 0.64000 2500 ; GLY(55)-ASP(58) 2-4
56 61 1 0.64000 2500 ; VAL(56)-CYS(61) 2-4
58 63 1 0.64000 2500 ; ASP(58)-LYS(63) 2-4
122 128 1 0.64000 2500 ; LYS(122)-LEU(128) 1-3
126 130 1 0.64000 2500 ; PRO(126)-CYS(130) 2-4
128 132 1 0.64000 2500 ; LEU(128)-CYS(132) 2-4
142 149 1 0.64000 2500 ; ASP(142)-ALA(149) 1-3
145 150 1 0.64000 2500 ; GLN(145)-LEU(150) 2-4
149 152 1 0.64000 2500 ; ALA(149)-LEU(152) 2-4
150 154 1 0.64000 2500 ; LEU(150)-CYS(154) 2-4
152 156 1 0.64000 2500 ; LEU(152)-GLN(156) 2-4
154 160 1 0.64000 2500 ; CYS(154)-LYS(160) 2-4
; Long elastic bonds for extended regions
23 31 1 0.97000 2500 ; ASN(23)-CYS(31) 1-4
27 33 1 0.97000 2500 ; PRO(27)-CYS(33) 1-4
29 35 1 0.97000 2500 ; LEU(29)-ALA(35) 1-4
31 36 1 0.97000 2500 ; CYS(31)-THR(36) 1-4
33 40 1 0.97000 2500 ; CYS(33)-ASN(40) 1-4
35 44 1 0.97000 2500 ; ALA(35)-VAL(44) 1-4
53 58 1 0.97000 2500 ; ILE(53)-ASP(58) 1-4
55 61 1 0.97000 2500 ; GLY(55)-CYS(61) 1-4
56 63 1 0.97000 2500 ; VAL(56)-LYS(63) 1-4
122 130 1 0.97000 2500 ; LYS(122)-CYS(130) 1-4
126 132 1 0.97000 2500 ; PRO(126)-CYS(132) 1-4
142 150 1 0.97000 2500 ; ASP(142)-LEU(150) 1-4
145 152 1 0.97000 2500 ; GLN(145)-LEU(152) 1-4
149 154 1 0.97000 2500 ; ALA(149)-CYS(154) 1-4
150 156 1 0.97000 2500 ; LEU(150)-GLN(156) 1-4
152 160 1 0.97000 2500 ; LEU(152)-LYS(160) 1-4
[ constraints ]
85 89 1 0.33000 ; THR(S)-GLY(1)
89 90 1 0.31000 ; GLY(1)-ALA(1)
90 91 1 0.31000 ; ALA(1)-ILE(1)
91 93 1 0.31000 ; ILE(1)-PHE(1)
93 97 1 0.31000 ; PHE(1)-GLN(H)
97 101 1 0.31000 ; GLN(H)-ALA(H)
101 102 1 0.31000 ; ALA(H)-HIS(2)
102 106 1 0.31000 ; HIS(2)-CYS(2)
106 108 1 0.31000 ; CYS(2)-ALA(2)
108 109 1 0.31000 ; ALA(2)-SER(2)
109 113 1 0.33000 ; SER(2)-LYS(T)
2 3 1 0.26500 ; VAL
10 11 1 0.28000 ; THR
16 17 1 0.27000 ; PHE
16 18 1 0.27000 ; PHE
17 18 1 0.27000 ; PHE
21 22 1 0.28000 ; SER
25 26 1 0.28000 ; ASN
38 39 1 0.28000 ; THR
42 43 1 0.28000 ; ASN
44 45 1 0.26500 ; VAL
49 50 1 0.11000 ; ASP
53 54 1 0.31000 ; ILE
56 57 1 0.26500 ; VAL
59 60 1 0.11000 ; ASP
65 66 1 0.11000 ; LYS
69 70 1 0.28000 ; THR
75 76 1 0.28000 ; THR
77 78 1 0.31000 ; ILE
80 81 1 0.26500 ; VAL
83 84 1 0.11000 ; ASP
87 88 1 0.28000 ; THR
91 92 1 0.31000 ; ILE
94 95 1 0.27000 ; PHE
94 96 1 0.27000 ; PHE
95 96 1 0.27000 ; PHE
99 100 1 0.28000 ; GLN
103 104 1 0.27000 ; HIS
103 105 1 0.27000 ; HIS
104 105 1 0.27000 ; HIS
111 112 1 0.28000 ; SER
115 116 1 0.11000 ; LYS
120 121 1 0.28000 ; SER
124 125 1 0.11000 ; LYS
134 135 1 0.26500 ; VAL
139 140 1 0.26500 ; VAL
143 144 1 0.11000 ; ASP
147 148 1 0.28000 ; GLN
158 159 1 0.28000 ; GLN
162 163 1 0.11000 ; LYS
165 166 1 0.31000 ; ILE
170 171 1 0.28000 ; THR
[ angles ]
; Backbone angles
1 2 4 2 127 25 ; ALA(C)-VAL(C)-CYS(S)
2 4 6 2 127 25 ; VAL(C)-CYS(S)-PRO(C)
4 6 8 2 127 25 ; CYS(S)-PRO(C)-THR(S)
6 8 12 2 127 25 ; PRO(C)-THR(S)-GLY(S)
8 12 13 2 100 25 ; THR(S)-GLY(S)-LEU(T)
12 13 15 2 100 25 ; GLY(S)-LEU(T)-PHE(T)
13 15 19 2 100 25 ; LEU(T)-PHE(T)-SER(C)
15 19 23 2 100 25 ; PHE(T)-SER(C)-ASN(E)
19 23 27 2 127 25 ; SER(C)-ASN(E)-PRO(E)
23 27 29 2 134 25 ; ASN(E)-PRO(E)-LEU(E)
27 29 31 2 134 25 ; PRO(E)-LEU(E)-CYS(E)
29 31 33 2 134 25 ; LEU(E)-CYS(E)-CYS(E)
31 33 35 2 134 25 ; CYS(E)-CYS(E)-ALA(E)
33 35 36 2 134 25 ; CYS(E)-ALA(E)-THR(E)
35 36 40 2 134 25 ; ALA(E)-THR(E)-ASN(E)
36 40 44 2 134 25 ; THR(E)-ASN(E)-VAL(E)
40 44 46 2 100 25 ; ASN(E)-VAL(E)-LEU(T)
44 46 48 2 100 25 ; VAL(E)-LEU(T)-ASP(T)
46 48 51 2 100 25 ; LEU(T)-ASP(T)-LEU(T)
48 51 53 2 100 25 ; ASP(T)-LEU(T)-ILE(E)
51 53 55 2 100 25 ; LEU(T)-ILE(E)-GLY(E)
53 55 56 2 134 25 ; ILE(E)-GLY(E)-VAL(E)
55 56 58 2 134 25 ; GLY(E)-VAL(E)-ASP(E)
56 58 61 2 134 25 ; VAL(E)-ASP(E)-CYS(E)
58 61 63 2 134 25 ; ASP(E)-CYS(E)-LYS(E)
61 63 67 2 127 25 ; CYS(E)-LYS(E)-THR(C)
63 67 71 2 127 25 ; LYS(E)-THR(C)-PRO(C)
67 71 73 2 127 25 ; THR(C)-PRO(C)-THR(S)
71 73 77 2 127 25 ; PRO(C)-THR(S)-ILE(S)
73 77 79 2 127 25 ; THR(S)-ILE(S)-ALA(C)
77 79 80 2 127 25 ; ILE(S)-ALA(C)-VAL(C)
79 80 82 2 127 25 ; ALA(C)-VAL(C)-ASP(C)
80 82 85 2 127 25 ; VAL(C)-ASP(C)-THR(S)
82 85 89 2 127 25 ; ASP(C)-THR(S)-GLY(1)
85 89 90 2 130 25 ; THR(S)-GLY(1)-ALA(1)
89 90 91 2 96 700 ; GLY(1)-ALA(1)-ILE(1)
90 91 93 2 96 700 ; ALA(1)-ILE(1)-PHE(1)
91 93 97 2 96 700 ; ILE(1)-PHE(1)-GLN(H)
93 97 101 2 96 700 ; PHE(1)-GLN(H)-ALA(H)
97 101 102 2 96 700 ; GLN(H)-ALA(H)-HIS(2)
101 102 106 2 96 700 ; ALA(H)-HIS(2)-CYS(2)
102 106 108 2 96 700 ; HIS(2)-CYS(2)-ALA(2)
106 108 109 2 96 700 ; CYS(2)-ALA(2)-SER(2)
108 109 113 2 100 25 ; ALA(2)-SER(2)-LYS(T)
109 113 117 2 100 25 ; SER(2)-LYS(T)-GLY(T)
113 117 118 2 100 25 ; LYS(T)-GLY(T)-SER(C)
117 118 122 2 100 25 ; GLY(T)-SER(C)-LYS(E)
118 122 126 2 127 25 ; SER(C)-LYS(E)-PRO(E)
122 126 128 2 134 25 ; LYS(E)-PRO(E)-LEU(E)
126 128 130 2 134 25 ; PRO(E)-LEU(E)-CYS(E)
128 130 132 2 134 25 ; LEU(E)-CYS(E)-CYS(E)
130 132 134 2 130 25 ; CYS(E)-CYS(E)-VAL(S)
132 134 136 2 127 25 ; CYS(E)-VAL(S)-ALA(C)
134 136 137 2 127 25 ; VAL(S)-ALA(C)-PRO(S)
136 137 139 2 127 25 ; ALA(C)-PRO(S)-VAL(S)
137 139 141 2 127 25 ; PRO(S)-VAL(S)-ALA(C)
139 141 142 2 127 25 ; VAL(S)-ALA(C)-ASP(E)
141 142 145 2 127 25 ; ALA(C)-ASP(E)-GLN(E)
142 145 149 2 134 25 ; ASP(E)-GLN(E)-ALA(E)
145 149 150 2 134 25 ; GLN(E)-ALA(E)-LEU(E)
149 150 152 2 134 25 ; ALA(E)-LEU(E)-LEU(E)
150 152 154 2 134 25 ; LEU(E)-LEU(E)-CYS(E)
152 154 156 2 134 25 ; LEU(E)-CYS(E)-GLN(E)
154 156 160 2 134 25 ; CYS(E)-GLN(E)-LYS(E)
156 160 164 2 127 25 ; GLN(E)-LYS(E)-ALA(C)
160 164 165 2 100 25 ; LYS(E)-ALA(C)-ILE(T)
164 165 167 2 100 25 ; ALA(C)-ILE(T)-GLY(T)
165 167 168 2 100 25 ; ILE(T)-GLY(T)-THR(C)
; Backbone-sidechain angles
1 2 3 2 100 25 ; ALA(C)-VAL(C) SBB
2 4 5 2 100 25 ; VAL(C)-CYS(S) SBB
4 6 7 2 100 25 ; CYS(S)-PRO(C) SBB
6 8 9 2 100 25 ; PRO(C)-THR(S) SBB
12 13 14 2 100 25 ; GLY(S)-LEU(T) SBB
13 15 16 2 100 25 ; LEU(T)-PHE(T) SBB
15 19 20 2 100 25 ; PHE(T)-SER(C) SBB
19 23 24 2 100 25 ; SER(C)-ASN(E) SBB
23 27 28 2 100 25 ; ASN(E)-PRO(E) SBB
27 29 30 2 100 25 ; PRO(E)-LEU(E) SBB
29 31 32 2 100 25 ; LEU(E)-CYS(E) SBB
31 33 34 2 100 25 ; CYS(E)-CYS(E) SBB
35 36 37 2 100 25 ; ALA(E)-THR(E) SBB
36 40 41 2 100 25 ; THR(E)-ASN(E) SBB
40 44 45 2 100 25 ; ASN(E)-VAL(E) SBB
44 46 47 2 100 25 ; VAL(E)-LEU(T) SBB
46 48 49 2 100 25 ; LEU(T)-ASP(T) SBB
48 51 52 2 100 25 ; ASP(T)-LEU(T) SBB
51 53 54 2 100 25 ; LEU(T)-ILE(E) SBB
55 56 57 2 100 25 ; GLY(E)-VAL(E) SBB
56 58 59 2 100 25 ; VAL(E)-ASP(E) SBB
58 61 62 2 100 25 ; ASP(E)-CYS(E) SBB
61 63 64 2 100 25 ; CYS(E)-LYS(E) SBB
63 67 68 2 100 25 ; LYS(E)-THR(C) SBB
67 71 72 2 100 25 ; THR(C)-PRO(C) SBB
71 73 74 2 100 25 ; PRO(C)-THR(S) SBB
73 77 78 2 100 25 ; THR(S)-ILE(S) SBB
79 80 81 2 100 25 ; ALA(C)-VAL(C) SBB
80 82 83 2 100 25 ; VAL(C)-ASP(C) SBB
82 85 86 2 100 25 ; ASP(C)-THR(S) SBB
90 91 92 2 100 25 ; ALA(1)-ILE(1) SBB
91 93 94 2 100 25 ; ILE(1)-PHE(1) SBB
93 97 98 2 100 25 ; PHE(1)-GLN(H) SBB
101 102 103 2 100 25 ; ALA(H)-HIS(2) SBB
102 106 107 2 100 25 ; HIS(2)-CYS(2) SBB
108 109 110 2 100 25 ; ALA(2)-SER(2) SBB
109 113 114 2 100 25 ; SER(2)-LYS(T) SBB
117 118 119 2 100 25 ; GLY(T)-SER(C) SBB
118 122 123 2 100 25 ; SER(C)-LYS(E) SBB
122 126 127 2 100 25 ; LYS(E)-PRO(E) SBB
126 128 129 2 100 25 ; PRO(E)-LEU(E) SBB
128 130 131 2 100 25 ; LEU(E)-CYS(E) SBB
130 132 133 2 100 25 ; CYS(E)-CYS(E) SBB
132 134 135 2 100 25 ; CYS(E)-VAL(S) SBB
136 137 138 2 100 25 ; ALA(C)-PRO(S) SBB
137 139 140 2 100 25 ; PRO(S)-VAL(S) SBB
141 142 143 2 100 25 ; ALA(C)-ASP(E) SBB
142 145 146 2 100 25 ; ASP(E)-GLN(E) SBB
149 150 151 2 100 25 ; ALA(E)-LEU(E) SBB
150 152 153 2 100 25 ; LEU(E)-LEU(E) SBB
152 154 155 2 100 25 ; LEU(E)-CYS(E) SBB
154 156 157 2 100 25 ; CYS(E)-GLN(E) SBB
156 160 161 2 100 25 ; GLN(E)-LYS(E) SBB
164 165 166 2 100 25 ; ALA(C)-ILE(T) SBB
167 168 169 2 100 25 ; GLY(T)-THR(C) SBB
; Sidechain angles
15 16 17 2 150 50 ; PHE
15 16 18 2 150 50 ; PHE
63 64 65 2 180 25 ; LYS
93 94 95 2 150 50 ; PHE
93 94 96 2 150 50 ; PHE
102 103 104 2 150 50 ; HIS
102 103 105 2 150 50 ; HIS
113 114 115 2 180 25 ; LYS
122 123 124 2 180 25 ; LYS
160 161 162 2 180 25 ; LYS
[ dihedrals ]
; Backbone dihedrals
89 90 91 93 1 -120 400 1 ; GLY(1)-ALA(1)-ILE(1)-PHE(1)
90 91 93 97 1 -120 400 1 ; ALA(1)-ILE(1)-PHE(1)-GLN(H)
91 93 97 101 1 -120 400 1 ; ILE(1)-PHE(1)-GLN(H)-ALA(H)
93 97 101 102 1 -120 400 1 ; PHE(1)-GLN(H)-ALA(H)-HIS(2)
97 101 102 106 1 -120 400 1 ; GLN(H)-ALA(H)-HIS(2)-CYS(2)
101 102 106 108 1 -120 400 1 ; ALA(H)-HIS(2)-CYS(2)-ALA(2)
102 106 108 109 1 -120 400 1 ; HIS(2)-CYS(2)-ALA(2)-SER(2)
; Sidechain improper dihedrals
15 17 18 16 2 0 50 ; PHE
93 95 96 94 2 0 50 ; PHE
102 104 105 103 2 0 50 ; HIS
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
2 1 POSRES_FC POSRES_FC POSRES_FC
4 1 POSRES_FC POSRES_FC POSRES_FC
6 1 POSRES_FC POSRES_FC POSRES_FC
8 1 POSRES_FC POSRES_FC POSRES_FC
12 1 POSRES_FC POSRES_FC POSRES_FC
13 1 POSRES_FC POSRES_FC POSRES_FC
15 1 POSRES_FC POSRES_FC POSRES_FC
19 1 POSRES_FC POSRES_FC POSRES_FC
23 1 POSRES_FC POSRES_FC POSRES_FC
27 1 POSRES_FC POSRES_FC POSRES_FC
29 1 POSRES_FC POSRES_FC POSRES_FC
31 1 POSRES_FC POSRES_FC POSRES_FC
33 1 POSRES_FC POSRES_FC POSRES_FC
35 1 POSRES_FC POSRES_FC POSRES_FC
36 1 POSRES_FC POSRES_FC POSRES_FC
40 1 POSRES_FC POSRES_FC POSRES_FC
44 1 POSRES_FC POSRES_FC POSRES_FC
46 1 POSRES_FC POSRES_FC POSRES_FC
48 1 POSRES_FC POSRES_FC POSRES_FC
51 1 POSRES_FC POSRES_FC POSRES_FC
53 1 POSRES_FC POSRES_FC POSRES_FC
55 1 POSRES_FC POSRES_FC POSRES_FC
56 1 POSRES_FC POSRES_FC POSRES_FC
58 1 POSRES_FC POSRES_FC POSRES_FC
61 1 POSRES_FC POSRES_FC POSRES_FC
63 1 POSRES_FC POSRES_FC POSRES_FC
67 1 POSRES_FC POSRES_FC POSRES_FC
71 1 POSRES_FC POSRES_FC POSRES_FC
73 1 POSRES_FC POSRES_FC POSRES_FC
77 1 POSRES_FC POSRES_FC POSRES_FC
79 1 POSRES_FC POSRES_FC POSRES_FC
80 1 POSRES_FC POSRES_FC POSRES_FC
82 1 POSRES_FC POSRES_FC POSRES_FC
85 1 POSRES_FC POSRES_FC POSRES_FC
89 1 POSRES_FC POSRES_FC POSRES_FC
90 1 POSRES_FC POSRES_FC POSRES_FC
91 1 POSRES_FC POSRES_FC POSRES_FC
93 1 POSRES_FC POSRES_FC POSRES_FC
97 1 POSRES_FC POSRES_FC POSRES_FC
101 1 POSRES_FC POSRES_FC POSRES_FC
102 1 POSRES_FC POSRES_FC POSRES_FC
106 1 POSRES_FC POSRES_FC POSRES_FC
108 1 POSRES_FC POSRES_FC POSRES_FC
109 1 POSRES_FC POSRES_FC POSRES_FC
113 1 POSRES_FC POSRES_FC POSRES_FC
117 1 POSRES_FC POSRES_FC POSRES_FC
118 1 POSRES_FC POSRES_FC POSRES_FC
122 1 POSRES_FC POSRES_FC POSRES_FC
126 1 POSRES_FC POSRES_FC POSRES_FC
128 1 POSRES_FC POSRES_FC POSRES_FC
130 1 POSRES_FC POSRES_FC POSRES_FC
132 1 POSRES_FC POSRES_FC POSRES_FC
134 1 POSRES_FC POSRES_FC POSRES_FC
136 1 POSRES_FC POSRES_FC POSRES_FC
137 1 POSRES_FC POSRES_FC POSRES_FC
139 1 POSRES_FC POSRES_FC POSRES_FC
141 1 POSRES_FC POSRES_FC POSRES_FC
142 1 POSRES_FC POSRES_FC POSRES_FC
145 1 POSRES_FC POSRES_FC POSRES_FC
149 1 POSRES_FC POSRES_FC POSRES_FC
150 1 POSRES_FC POSRES_FC POSRES_FC
152 1 POSRES_FC POSRES_FC POSRES_FC
154 1 POSRES_FC POSRES_FC POSRES_FC
156 1 POSRES_FC POSRES_FC POSRES_FC
160 1 POSRES_FC POSRES_FC POSRES_FC
164 1 POSRES_FC POSRES_FC POSRES_FC
165 1 POSRES_FC POSRES_FC POSRES_FC
167 1 POSRES_FC POSRES_FC POSRES_FC
168 1 POSRES_FC POSRES_FC POSRES_FC
#endif
; Created by py version 2.6
; Using the following options: -f Protein.pdb -ss Protein.dssp -p backbone -ff martini22p -o topol.top -x Protein_CG.pdb -v
; Sequence:
; AVCPTGLFSNPLCCATNVLDLIGVDCKTPTIAVDTGAIFQAHCASKGSKPLCCVAPVADQALLCQKAIGT
; Secondary Structure:
; CCSCSSTTCEEEEEEEEETTTEEEEEECCSSCCCS1111HH2222TTCEEEEESCSSCEEEEEEEECTTC
[ moleculetype ]
; Name Exclusions
Protein_A 1
[ atoms ]
1 Qd 1 ALA BB 1 1.0000 ; C
2 P5 2 VAL BB 2 0.0000 ; C
3 C2 2 VAL SC1 3 0.0000 ; C
4 P5 3 CYS BB 4 0.0000 ; S
5 C5 3 CYS SC1 5 0.0000 ; S
6 P4 4 PRO BB 6 0.0000 ; C
7 C3 4 PRO SC1 7 0.0000 ; C
8 P5 5 THR BB 8 0.0000 ; S
9 N0 5 THR SC1 9 0.0000 0.0000 ; S
10 D 5 THR SCP 10 0.3600 36.0000 ; S
11 D 5 THR SCN 11 -0.3600 36.0000 ; S
12 P5 6 GLY BB 12 0.0000 ; S
13 Nda 7 LEU BB 13 0.0000 ; T
14 C1 7 LEU SC1 14 0.0000 ; T
15 Nda 8 PHE BB 15 0.0000 ; T
16 SC5 8 PHE SC1 16 0.0000 ; T
17 SC5 8 PHE SC2 17 0.0000 ; T
18 SC5 8 PHE SC3 18 0.0000 ; T
19 P5 9 SER BB 19 0.0000 ; C
20 N0 9 SER SC1 20 0.0000 0.0000 ; C
21 D 9 SER SCP 21 0.4000 36.0000 ; C
22 D 9 SER SCN 22 -0.4000 36.0000 ; C
23 Nda 10 ASN BB 23 0.0000 ; E
24 Nda 10 ASN SC1 24 0.0000 0.0000 ; E
25 D 10 ASN SCP 25 0.4600 36.0000 ; E
26 D 10 ASN SCN 26 -0.4600 36.0000 ; E
27 N0 11 PRO BB 27 0.0000 ; E
28 C3 11 PRO SC1 28 0.0000 ; E
29 Nda 12 LEU BB 29 0.0000 ; E
30 C1 12 LEU SC1 30 0.0000 ; E
31 Nda 13 CYS BB 31 0.0000 ; E
32 C5 13 CYS SC1 32 0.0000 ; E
33 Nda 14 CYS BB 33 0.0000 ; E
34 C5 14 CYS SC1 34 0.0000 ; E
35 N0 15 ALA BB 35 0.0000 ; E
36 Nda 16 THR BB 36 0.0000 ; E
37 N0 16 THR SC1 37 0.0000 0.0000 ; E
38 D 16 THR SCP 38 0.3600 36.0000 ; E
39 D 16 THR SCN 39 -0.3600 36.0000 ; E
40 Nda 17 ASN BB 40 0.0000 ; E
41 Nda 17 ASN SC1 41 0.0000 0.0000 ; E
42 D 17 ASN SCP 42 0.4600 36.0000 ; E
43 D 17 ASN SCN 43 -0.4600 36.0000 ; E
44 Nda 18 VAL BB 44 0.0000 ; E
45 C2 18 VAL SC1 45 0.0000 ; E
46 Nda 19 LEU BB 46 0.0000 ; T
47 C1 19 LEU SC1 47 0.0000 ; T
48 Nda 20 ASP BB 48 0.0000 ; T
49 Qa 20 ASP SC1 49 0.0000 36.0000 ; T
50 D 20 ASP SCN 50 -1.0000 36.0000 ; T
51 Nda 21 LEU BB 51 0.0000 ; T
52 C1 21 LEU SC1 52 0.0000 ; T
53 Nda 22 ILE BB 53 0.0000 ; E
54 C1 22 ILE SC1 54 0.0000 ; E
55 Nda 23 GLY BB 55 0.0000 ; E
56 Nda 24 VAL BB 56 0.0000 ; E
57 C2 24 VAL SC1 57 0.0000 ; E
58 Nda 25 ASP BB 58 0.0000 ; E
59 Qa 25 ASP SC1 59 0.0000 36.0000 ; E
60 D 25 ASP SCN 60 -1.0000 36.0000 ; E
61 Nda 26 CYS BB 61 0.0000 ; E
62 C5 26 CYS SC1 62 0.0000 ; E
63 Nda 27 LYS BB 63 0.0000 ; E
64 C3 27 LYS SC1 64 0.0000 72.0000 ; E
65 Qd 27 LYS SC2 65 0.0000 36.0000 ; E
66 D 27 LYS SCP 66 1.0000 36.0000 ; E
67 P5 28 THR BB 67 0.0000 ; C
68 N0 28 THR SC1 68 0.0000 0.0000 ; C
69 D 28 THR SCP 69 0.3600 36.0000 ; C
70 D 28 THR SCN 70 -0.3600 36.0000 ; C
71 P4 29 PRO BB 71 0.0000 ; C
72 C3 29 PRO SC1 72 0.0000 ; C
73 P5 30 THR BB 73 0.0000 ; S
74 N0 30 THR SC1 74 0.0000 0.0000 ; S
75 D 30 THR SCP 75 0.3600 36.0000 ; S
76 D 30 THR SCN 76 -0.3600 36.0000 ; S
77 P5 31 ILE BB 77 0.0000 ; S
78 C1 31 ILE SC1 78 0.0000 ; S
79 P4 32 ALA BB 79 0.0000 ; C
80 P5 33 VAL BB 80 0.0000 ; C
81 C2 33 VAL SC1 81 0.0000 ; C
82 P5 34 ASP BB 82 0.0000 ; C
83 Qa 34 ASP SC1 83 0.0000 36.0000 ; C
84 D 34 ASP SCN 84 -1.0000 36.0000 ; C
85 P5 35 THR BB 85 0.0000 ; S
86 N0 35 THR SC1 86 0.0000 0.0000 ; S
87 D 35 THR SCP 87 0.3600 36.0000 ; S
88 D 35 THR SCN 88 -0.3600 36.0000 ; S
89 Nd 36 GLY BB 89 0.0000 ; 1
90 N0 37 ALA BB 90 0.0000 ; 1
91 Nd 38 ILE BB 91 0.0000 ; 1
92 C1 38 ILE SC1 92 0.0000 ; 1
93 Nd 39 PHE BB 93 0.0000 ; 1
94 SC5 39 PHE SC1 94 0.0000 ; 1
95 SC5 39 PHE SC2 95 0.0000 ; 1
96 SC5 39 PHE SC3 96 0.0000 ; 1
97 N0 40 GLN BB 97 0.0000 ; H
98 Nda 40 GLN SC1 98 0.0000 0.0000 ; H
99 D 40 GLN SCP 99 0.4200 36.0000 ; H
100 D 40 GLN SCN 100 -0.4200 36.0000 ; H
101 C5 41 ALA BB 101 0.0000 ; H
102 Na 42 HIS BB 102 0.0000 ; 2
103 SC4 42 HIS SC1 103 0.0000 ; 2
104 SP1 42 HIS SC2 104 0.0000 ; 2
105 SP1 42 HIS SC3 105 0.0000 ; 2
106 Na 43 CYS BB 106 0.0000 ; 2
107 C5 43 CYS SC1 107 0.0000 ; 2
108 N0 44 ALA BB 108 0.0000 ; 2
109 Na 45 SER BB 109 0.0000 ; 2
110 N0 45 SER SC1 110 0.0000 0.0000 ; 2
111 D 45 SER SCP 111 0.4000 36.0000 ; 2
112 D 45 SER SCN 112 -0.4000 36.0000 ; 2
113 Nda 46 LYS BB 113 0.0000 ; T
114 C3 46 LYS SC1 114 0.0000 72.0000 ; T
115 Qd 46 LYS SC2 115 0.0000 36.0000 ; T
116 D 46 LYS SCP 116 1.0000 36.0000 ; T
117 Nda 47 GLY BB 117 0.0000 ; T
118 P5 48 SER BB 118 0.0000 ; C
119 N0 48 SER SC1 119 0.0000 0.0000 ; C
120 D 48 SER SCP 120 0.4000 36.0000 ; C
121 D 48 SER SCN 121 -0.4000 36.0000 ; C
122 Nda 49 LYS BB 122 0.0000 ; E
123 C3 49 LYS SC1 123 0.0000 72.0000 ; E
124 Qd 49 LYS SC2 124 0.0000 36.0000 ; E
125 D 49 LYS SCP 125 1.0000 36.0000 ; E
126 N0 50 PRO BB 126 0.0000 ; E
127 C3 50 PRO SC1 127 0.0000 ; E
128 Nda 51 LEU BB 128 0.0000 ; E
129 C1 51 LEU SC1 129 0.0000 ; E
130 Nda 52 CYS BB 130 0.0000 ; E
131 C5 52 CYS SC1 131 0.0000 ; E
132 Nda 53 CYS BB 132 0.0000 ; E
133 C5 53 CYS SC1 133 0.0000 ; E
134 P5 54 VAL BB 134 0.0000 ; S
135 C2 54 VAL SC1 135 0.0000 ; S
136 P4 55 ALA BB 136 0.0000 ; C
137 P4 56 PRO BB 137 0.0000 ; S
138 C3 56 PRO SC1 138 0.0000 ; S
139 P5 57 VAL BB 139 0.0000 ; S
140 C2 57 VAL SC1 140 0.0000 ; S
141 P4 58 ALA BB 141 0.0000 ; C
142 Nda 59 ASP BB 142 0.0000 ; E
143 Qa 59 ASP SC1 143 0.0000 36.0000 ; E
144 D 59 ASP SCN 144 -1.0000 36.0000 ; E
145 Nda 60 GLN BB 145 0.0000 ; E
146 Nda 60 GLN SC1 146 0.0000 0.0000 ; E
147 D 60 GLN SCP 147 0.4200 36.0000 ; E
148 D 60 GLN SCN 148 -0.4200 36.0000 ; E
149 N0 61 ALA BB 149 0.0000 ; E
150 Nda 62 LEU BB 150 0.0000 ; E
151 C1 62 LEU SC1 151 0.0000 ; E
152 Nda 63 LEU BB 152 0.0000 ; E
153 C1 63 LEU SC1 153 0.0000 ; E
154 Nda 64 CYS BB 154 0.0000 ; E
155 C5 64 CYS SC1 155 0.0000 ; E
156 Nda 65 GLN BB 156 0.0000 ; E
157 Nda 65 GLN SC1 157 0.0000 0.0000 ; E
158 D 65 GLN SCP 158 0.4200 36.0000 ; E
159 D 65 GLN SCN 159 -0.4200 36.0000 ; E
160 Nda 66 LYS BB 160 0.0000 ; E
161 C3 66 LYS SC1 161 0.0000 72.0000 ; E
162 Qd 66 LYS SC2 162 0.0000 36.0000 ; E
163 D 66 LYS SCP 163 1.0000 36.0000 ; E
164 P4 67 ALA BB 164 0.0000 ; C
165 Nda 68 ILE BB 165 0.0000 ; T
166 C1 68 ILE SC1 166 0.0000 ; T
167 Nda 69 GLY BB 167 0.0000 ; T
168 Qa 70 THR BB 168 -1.0000 ; C
169 N0 70 THR SC1 169 0.0000 0.0000 ; C
170 D 70 THR SCP 170 0.3600 36.0000 ; C
171 D 70 THR SCN 171 -0.3600 36.0000 ; C
[ virtual_sites2 ]
9 10 11 1 0.50000 ; THR
20 21 22 1 0.50000 ; SER
24 25 26 1 0.50000 ; ASN
37 38 39 1 0.50000 ; THR
41 42 43 1 0.50000 ; ASN
68 69 70 1 0.50000 ; THR
74 75 76 1 0.50000 ; THR
86 87 88 1 0.50000 ; THR
98 99 100 1 0.50000 ; GLN
110 111 112 1 0.50000 ; SER
119 120 121 1 0.50000 ; SER
146 147 148 1 0.50000 ; GLN
157 158 159 1 0.50000 ; GLN
169 170 171 1 0.50000 ; THR
[ exclusions ]
168 170 ; THR(70)
168 171 ; THR(70)
[ bonds ]
; Backbone bonds
1 2 1 0.35000 1250 ; ALA(C)-VAL(C)
2 4 1 0.35000 1250 ; VAL(C)-CYS(S)
4 6 1 0.35000 1250 ; CYS(S)-PRO(C)
6 8 1 0.35000 1250 ; PRO(C)-THR(S)
8 12 1 0.35000 1250 ; THR(S)-GLY(S)
12 13 1 0.35000 1250 ; GLY(S)-LEU(T)
13 15 1 0.35000 1250 ; LEU(T)-PHE(T)
15 19 1 0.35000 1250 ; PHE(T)-SER(C)
19 23 1 0.35000 1250 ; SER(C)-ASN(E)
23 27 1 0.35000 1250 ; ASN(E)-PRO(E)
27 29 1 0.35000 1250 ; PRO(E)-LEU(E)
29 31 1 0.35000 1250 ; LEU(E)-CYS(E)
31 33 1 0.35000 1250 ; CYS(E)-CYS(E)
33 35 1 0.35000 1250 ; CYS(E)-ALA(E)
35 36 1 0.35000 1250 ; ALA(E)-THR(E)
36 40 1 0.35000 1250 ; THR(E)-ASN(E)
40 44 1 0.35000 1250 ; ASN(E)-VAL(E)
44 46 1 0.35000 1250 ; VAL(E)-LEU(T)
46 48 1 0.35000 1250 ; LEU(T)-ASP(T)
48 51 1 0.35000 1250 ; ASP(T)-LEU(T)
51 53 1 0.35000 1250 ; LEU(T)-ILE(E)
53 55 1 0.35000 1250 ; ILE(E)-GLY(E)
55 56 1 0.35000 1250 ; GLY(E)-VAL(E)
56 58 1 0.35000 1250 ; VAL(E)-ASP(E)
58 61 1 0.35000 1250 ; ASP(E)-CYS(E)
61 63 1 0.35000 1250 ; CYS(E)-LYS(E)
63 67 1 0.35000 1250 ; LYS(E)-THR(C)
67 71 1 0.35000 1250 ; THR(C)-PRO(C)
71 73 1 0.35000 1250 ; PRO(C)-THR(S)
73 77 1 0.35000 1250 ; THR(S)-ILE(S)
77 79 1 0.35000 1250 ; ILE(S)-ALA(C)
79 80 1 0.35000 1250 ; ALA(C)-VAL(C)
80 82 1 0.35000 1250 ; VAL(C)-ASP(C)
82 85 1 0.35000 1250 ; ASP(C)-THR(S)
113 117 1 0.35000 1250 ; LYS(T)-GLY(T)
117 118 1 0.35000 1250 ; GLY(T)-SER(C)
118 122 1 0.35000 1250 ; SER(C)-LYS(E)
122 126 1 0.35000 1250 ; LYS(E)-PRO(E)
126 128 1 0.35000 1250 ; PRO(E)-LEU(E)
128 130 1 0.35000 1250 ; LEU(E)-CYS(E)
130 132 1 0.35000 1250 ; CYS(E)-CYS(E)
132 134 1 0.35000 1250 ; CYS(E)-VAL(S)
134 136 1 0.35000 1250 ; VAL(S)-ALA(C)
136 137 1 0.35000 1250 ; ALA(C)-PRO(S)
137 139 1 0.35000 1250 ; PRO(S)-VAL(S)
139 141 1 0.35000 1250 ; VAL(S)-ALA(C)
141 142 1 0.35000 1250 ; ALA(C)-ASP(E)
142 145 1 0.35000 1250 ; ASP(E)-GLN(E)
145 149 1 0.35000 1250 ; GLN(E)-ALA(E)
149 150 1 0.35000 1250 ; ALA(E)-LEU(E)
150 152 1 0.35000 1250 ; LEU(E)-LEU(E)
152 154 1 0.35000 1250 ; LEU(E)-CYS(E)
154 156 1 0.35000 1250 ; CYS(E)-GLN(E)
156 160 1 0.35000 1250 ; GLN(E)-LYS(E)
160 164 1 0.35000 1250 ; LYS(E)-ALA(C)
164 165 1 0.35000 1250 ; ALA(C)-ILE(T)
165 167 1 0.35000 1250 ; ILE(T)-GLY(T)
167 168 1 0.35000 1250 ; GLY(T)-THR(C)
; Sidechain bonds
4 5 1 0.31000 7500 ; CYS
6 7 1 0.30000 7500 ; PRO
8 9 1 0.26000 9000 ; THR
13 14 1 0.33000 7500 ; LEU
15 16 1 0.31000 7500 ; PHE
19 20 1 0.25000 7500 ; SER
23 24 1 0.32000 5000 ; ASN
27 28 1 0.30000 7500 ; PRO
29 30 1 0.33000 7500 ; LEU
31 32 1 0.31000 7500 ; CYS
33 34 1 0.31000 7500 ; CYS
36 37 1 0.26000 9000 ; THR
40 41 1 0.32000 5000 ; ASN
46 47 1 0.33000 7500 ; LEU
48 49 1 0.32000 7500 ; ASP
51 52 1 0.33000 7500 ; LEU
58 59 1 0.32000 7500 ; ASP
61 62 1 0.31000 7500 ; CYS
63 64 1 0.33000 5000 ; LYS
64 65 1 0.28000 5000 ; LYS
67 68 1 0.26000 9000 ; THR
71 72 1 0.30000 7500 ; PRO
73 74 1 0.26000 9000 ; THR
82 83 1 0.32000 7500 ; ASP
85 86 1 0.26000 9000 ; THR
93 94 1 0.31000 7500 ; PHE
97 98 1 0.40000 5000 ; GLN
102 103 1 0.32000 7500 ; HIS
106 107 1 0.31000 7500 ; CYS
109 110 1 0.25000 7500 ; SER
113 114 1 0.33000 5000 ; LYS
114 115 1 0.28000 5000 ; LYS
118 119 1 0.25000 7500 ; SER
122 123 1 0.33000 5000 ; LYS
123 124 1 0.28000 5000 ; LYS
126 127 1 0.30000 7500 ; PRO
128 129 1 0.33000 7500 ; LEU
130 131 1 0.31000 7500 ; CYS
132 133 1 0.31000 7500 ; CYS
137 138 1 0.30000 7500 ; PRO
142 143 1 0.32000 7500 ; ASP
145 146 1 0.40000 5000 ; GLN
150 151 1 0.33000 7500 ; LEU
152 153 1 0.33000 7500 ; LEU
154 155 1 0.31000 7500 ; CYS
156 157 1 0.40000 5000 ; GLN
160 161 1 0.33000 5000 ; LYS
161 162 1 0.28000 5000 ; LYS
168 169 1 0.26000 9000 ; THR
; Short elastic bonds for extended regions
23 29 1 0.64000 2500 ; ASN(23)-LEU(29) 1-3
27 31 1 0.64000 2500 ; PRO(27)-CYS(31) 2-4
29 33 1 0.64000 2500 ; LEU(29)-CYS(33) 2-4
31 35 1 0.64000 2500 ; CYS(31)-ALA(35) 2-4
33 36 1 0.64000 2500 ; CYS(33)-THR(36) 2-4
35 40 1 0.64000 2500 ; ALA(35)-ASN(40) 2-4
36 44 1 0.64000 2500 ; THR(36)-VAL(44) 2-4
53 56 1 0.64000 2500 ; ILE(53)-VAL(56) 1-3
55 58 1 0.64000 2500 ; GLY(55)-ASP(58) 2-4
56 61 1 0.64000 2500 ; VAL(56)-CYS(61) 2-4
58 63 1 0.64000 2500 ; ASP(58)-LYS(63) 2-4
122 128 1 0.64000 2500 ; LYS(122)-LEU(128) 1-3
126 130 1 0.64000 2500 ; PRO(126)-CYS(130) 2-4
128 132 1 0.64000 2500 ; LEU(128)-CYS(132) 2-4
142 149 1 0.64000 2500 ; ASP(142)-ALA(149) 1-3
145 150 1 0.64000 2500 ; GLN(145)-LEU(150) 2-4
149 152 1 0.64000 2500 ; ALA(149)-LEU(152) 2-4
150 154 1 0.64000 2500 ; LEU(150)-CYS(154) 2-4
152 156 1 0.64000 2500 ; LEU(152)-GLN(156) 2-4
154 160 1 0.64000 2500 ; CYS(154)-LYS(160) 2-4
; Long elastic bonds for extended regions
23 31 1 0.97000 2500 ; ASN(23)-CYS(31) 1-4
27 33 1 0.97000 2500 ; PRO(27)-CYS(33) 1-4
29 35 1 0.97000 2500 ; LEU(29)-ALA(35) 1-4
31 36 1 0.97000 2500 ; CYS(31)-THR(36) 1-4
33 40 1 0.97000 2500 ; CYS(33)-ASN(40) 1-4
35 44 1 0.97000 2500 ; ALA(35)-VAL(44) 1-4
53 58 1 0.97000 2500 ; ILE(53)-ASP(58) 1-4
55 61 1 0.97000 2500 ; GLY(55)-CYS(61) 1-4
56 63 1 0.97000 2500 ; VAL(56)-LYS(63) 1-4
122 130 1 0.97000 2500 ; LYS(122)-CYS(130) 1-4
126 132 1 0.97000 2500 ; PRO(126)-CYS(132) 1-4
142 150 1 0.97000 2500 ; ASP(142)-LEU(150) 1-4
145 152 1 0.97000 2500 ; GLN(145)-LEU(152) 1-4
149 154 1 0.97000 2500 ; ALA(149)-CYS(154) 1-4
150 156 1 0.97000 2500 ; LEU(150)-GLN(156) 1-4
152 160 1 0.97000 2500 ; LEU(152)-LYS(160) 1-4
[ constraints ]
85 89 1 0.33000 ; THR(S)-GLY(1)
89 90 1 0.31000 ; GLY(1)-ALA(1)
90 91 1 0.31000 ; ALA(1)-ILE(1)
91 93 1 0.31000 ; ILE(1)-PHE(1)
93 97 1 0.31000 ; PHE(1)-GLN(H)
97 101 1 0.31000 ; GLN(H)-ALA(H)
101 102 1 0.31000 ; ALA(H)-HIS(2)
102 106 1 0.31000 ; HIS(2)-CYS(2)
106 108 1 0.31000 ; CYS(2)-ALA(2)
108 109 1 0.31000 ; ALA(2)-SER(2)
109 113 1 0.33000 ; SER(2)-LYS(T)
2 3 1 0.26500 ; VAL
10 11 1 0.28000 ; THR
16 17 1 0.27000 ; PHE
16 18 1 0.27000 ; PHE
17 18 1 0.27000 ; PHE
21 22 1 0.28000 ; SER
25 26 1 0.28000 ; ASN
38 39 1 0.28000 ; THR
42 43 1 0.28000 ; ASN
44 45 1 0.26500 ; VAL
49 50 1 0.11000 ; ASP
53 54 1 0.31000 ; ILE
56 57 1 0.26500 ; VAL
59 60 1 0.11000 ; ASP
65 66 1 0.11000 ; LYS
69 70 1 0.28000 ; THR
75 76 1 0.28000 ; THR
77 78 1 0.31000 ; ILE
80 81 1 0.26500 ; VAL
83 84 1 0.11000 ; ASP
87 88 1 0.28000 ; THR
91 92 1 0.31000 ; ILE
94 95 1 0.27000 ; PHE
94 96 1 0.27000 ; PHE
95 96 1 0.27000 ; PHE
99 100 1 0.28000 ; GLN
103 104 1 0.27000 ; HIS
103 105 1 0.27000 ; HIS
104 105 1 0.27000 ; HIS
111 112 1 0.28000 ; SER
115 116 1 0.11000 ; LYS
120 121 1 0.28000 ; SER
124 125 1 0.11000 ; LYS
134 135 1 0.26500 ; VAL
139 140 1 0.26500 ; VAL
143 144 1 0.11000 ; ASP
147 148 1 0.28000 ; GLN
158 159 1 0.28000 ; GLN
162 163 1 0.11000 ; LYS
165 166 1 0.31000 ; ILE
170 171 1 0.28000 ; THR
[ angles ]
; Backbone angles
1 2 4 2 127 25 ; ALA(C)-VAL(C)-CYS(S)
2 4 6 2 127 25 ; VAL(C)-CYS(S)-PRO(C)
4 6 8 2 127 25 ; CYS(S)-PRO(C)-THR(S)
6 8 12 2 127 25 ; PRO(C)-THR(S)-GLY(S)
8 12 13 2 100 25 ; THR(S)-GLY(S)-LEU(T)
12 13 15 2 100 25 ; GLY(S)-LEU(T)-PHE(T)
13 15 19 2 100 25 ; LEU(T)-PHE(T)-SER(C)
15 19 23 2 100 25 ; PHE(T)-SER(C)-ASN(E)
19 23 27 2 127 25 ; SER(C)-ASN(E)-PRO(E)
23 27 29 2 134 25 ; ASN(E)-PRO(E)-LEU(E)
27 29 31 2 134 25 ; PRO(E)-LEU(E)-CYS(E)
29 31 33 2 134 25 ; LEU(E)-CYS(E)-CYS(E)
31 33 35 2 134 25 ; CYS(E)-CYS(E)-ALA(E)
33 35 36 2 134 25 ; CYS(E)-ALA(E)-THR(E)
35 36 40 2 134 25 ; ALA(E)-THR(E)-ASN(E)
36 40 44 2 134 25 ; THR(E)-ASN(E)-VAL(E)
40 44 46 2 100 25 ; ASN(E)-VAL(E)-LEU(T)
44 46 48 2 100 25 ; VAL(E)-LEU(T)-ASP(T)
46 48 51 2 100 25 ; LEU(T)-ASP(T)-LEU(T)
48 51 53 2 100 25 ; ASP(T)-LEU(T)-ILE(E)
51 53 55 2 100 25 ; LEU(T)-ILE(E)-GLY(E)
53 55 56 2 134 25 ; ILE(E)-GLY(E)-VAL(E)
55 56 58 2 134 25 ; GLY(E)-VAL(E)-ASP(E)
56 58 61 2 134 25 ; VAL(E)-ASP(E)-CYS(E)
58 61 63 2 134 25 ; ASP(E)-CYS(E)-LYS(E)
61 63 67 2 127 25 ; CYS(E)-LYS(E)-THR(C)
63 67 71 2 127 25 ; LYS(E)-THR(C)-PRO(C)
67 71 73 2 127 25 ; THR(C)-PRO(C)-THR(S)
71 73 77 2 127 25 ; PRO(C)-THR(S)-ILE(S)
73 77 79 2 127 25 ; THR(S)-ILE(S)-ALA(C)
77 79 80 2 127 25 ; ILE(S)-ALA(C)-VAL(C)
79 80 82 2 127 25 ; ALA(C)-VAL(C)-ASP(C)
80 82 85 2 127 25 ; VAL(C)-ASP(C)-THR(S)
82 85 89 2 127 25 ; ASP(C)-THR(S)-GLY(1)
85 89 90 2 130 25 ; THR(S)-GLY(1)-ALA(1)
89 90 91 2 96 700 ; GLY(1)-ALA(1)-ILE(1)
90 91 93 2 96 700 ; ALA(1)-ILE(1)-PHE(1)
91 93 97 2 96 700 ; ILE(1)-PHE(1)-GLN(H)
93 97 101 2 96 700 ; PHE(1)-GLN(H)-ALA(H)
97 101 102 2 96 700 ; GLN(H)-ALA(H)-HIS(2)
101 102 106 2 96 700 ; ALA(H)-HIS(2)-CYS(2)
102 106 108 2 96 700 ; HIS(2)-CYS(2)-ALA(2)
106 108 109 2 96 700 ; CYS(2)-ALA(2)-SER(2)
108 109 113 2 100 25 ; ALA(2)-SER(2)-LYS(T)
109 113 117 2 100 25 ; SER(2)-LYS(T)-GLY(T)
113 117 118 2 100 25 ; LYS(T)-GLY(T)-SER(C)
117 118 122 2 100 25 ; GLY(T)-SER(C)-LYS(E)
118 122 126 2 127 25 ; SER(C)-LYS(E)-PRO(E)
122 126 128 2 134 25 ; LYS(E)-PRO(E)-LEU(E)
126 128 130 2 134 25 ; PRO(E)-LEU(E)-CYS(E)
128 130 132 2 134 25 ; LEU(E)-CYS(E)-CYS(E)
130 132 134 2 130 25 ; CYS(E)-CYS(E)-VAL(S)
132 134 136 2 127 25 ; CYS(E)-VAL(S)-ALA(C)
134 136 137 2 127 25 ; VAL(S)-ALA(C)-PRO(S)
136 137 139 2 127 25 ; ALA(C)-PRO(S)-VAL(S)
137 139 141 2 127 25 ; PRO(S)-VAL(S)-ALA(C)
139 141 142 2 127 25 ; VAL(S)-ALA(C)-ASP(E)
141 142 145 2 127 25 ; ALA(C)-ASP(E)-GLN(E)
142 145 149 2 134 25 ; ASP(E)-GLN(E)-ALA(E)
145 149 150 2 134 25 ; GLN(E)-ALA(E)-LEU(E)
149 150 152 2 134 25 ; ALA(E)-LEU(E)-LEU(E)
150 152 154 2 134 25 ; LEU(E)-LEU(E)-CYS(E)
152 154 156 2 134 25 ; LEU(E)-CYS(E)-GLN(E)
154 156 160 2 134 25 ; CYS(E)-GLN(E)-LYS(E)
156 160 164 2 127 25 ; GLN(E)-LYS(E)-ALA(C)
160 164 165 2 100 25 ; LYS(E)-ALA(C)-ILE(T)
164 165 167 2 100 25 ; ALA(C)-ILE(T)-GLY(T)
165 167 168 2 100 25 ; ILE(T)-GLY(T)-THR(C)
; Backbone-sidechain angles
1 2 3 2 100 25 ; ALA(C)-VAL(C) SBB
2 4 5 2 100 25 ; VAL(C)-CYS(S) SBB
4 6 7 2 100 25 ; CYS(S)-PRO(C) SBB
6 8 9 2 100 25 ; PRO(C)-THR(S) SBB
12 13 14 2 100 25 ; GLY(S)-LEU(T) SBB
13 15 16 2 100 25 ; LEU(T)-PHE(T) SBB
15 19 20 2 100 25 ; PHE(T)-SER(C) SBB
19 23 24 2 100 25 ; SER(C)-ASN(E) SBB
23 27 28 2 100 25 ; ASN(E)-PRO(E) SBB
27 29 30 2 100 25 ; PRO(E)-LEU(E) SBB
29 31 32 2 100 25 ; LEU(E)-CYS(E) SBB
31 33 34 2 100 25 ; CYS(E)-CYS(E) SBB
35 36 37 2 100 25 ; ALA(E)-THR(E) SBB
36 40 41 2 100 25 ; THR(E)-ASN(E) SBB
40 44 45 2 100 25 ; ASN(E)-VAL(E) SBB
44 46 47 2 100 25 ; VAL(E)-LEU(T) SBB
46 48 49 2 100 25 ; LEU(T)-ASP(T) SBB
48 51 52 2 100 25 ; ASP(T)-LEU(T) SBB
51 53 54 2 100 25 ; LEU(T)-ILE(E) SBB
55 56 57 2 100 25 ; GLY(E)-VAL(E) SBB
56 58 59 2 100 25 ; VAL(E)-ASP(E) SBB
58 61 62 2 100 25 ; ASP(E)-CYS(E) SBB
61 63 64 2 100 25 ; CYS(E)-LYS(E) SBB
63 67 68 2 100 25 ; LYS(E)-THR(C) SBB
67 71 72 2 100 25 ; THR(C)-PRO(C) SBB
71 73 74 2 100 25 ; PRO(C)-THR(S) SBB
73 77 78 2 100 25 ; THR(S)-ILE(S) SBB
79 80 81 2 100 25 ; ALA(C)-VAL(C) SBB
80 82 83 2 100 25 ; VAL(C)-ASP(C) SBB
82 85 86 2 100 25 ; ASP(C)-THR(S) SBB
90 91 92 2 100 25 ; ALA(1)-ILE(1) SBB
91 93 94 2 100 25 ; ILE(1)-PHE(1) SBB
93 97 98 2 100 25 ; PHE(1)-GLN(H) SBB
101 102 103 2 100 25 ; ALA(H)-HIS(2) SBB
102 106 107 2 100 25 ; HIS(2)-CYS(2) SBB
108 109 110 2 100 25 ; ALA(2)-SER(2) SBB
109 113 114 2 100 25 ; SER(2)-LYS(T) SBB
117 118 119 2 100 25 ; GLY(T)-SER(C) SBB
118 122 123 2 100 25 ; SER(C)-LYS(E) SBB
122 126 127 2 100 25 ; LYS(E)-PRO(E) SBB
126 128 129 2 100 25 ; PRO(E)-LEU(E) SBB
128 130 131 2 100 25 ; LEU(E)-CYS(E) SBB
130 132 133 2 100 25 ; CYS(E)-CYS(E) SBB
132 134 135 2 100 25 ; CYS(E)-VAL(S) SBB
136 137 138 2 100 25 ; ALA(C)-PRO(S) SBB
137 139 140 2 100 25 ; PRO(S)-VAL(S) SBB
141 142 143 2 100 25 ; ALA(C)-ASP(E) SBB
142 145 146 2 100 25 ; ASP(E)-GLN(E) SBB
149 150 151 2 100 25 ; ALA(E)-LEU(E) SBB
150 152 153 2 100 25 ; LEU(E)-LEU(E) SBB
152 154 155 2 100 25 ; LEU(E)-CYS(E) SBB
154 156 157 2 100 25 ; CYS(E)-GLN(E) SBB
156 160 161 2 100 25 ; GLN(E)-LYS(E) SBB
164 165 166 2 100 25 ; ALA(C)-ILE(T) SBB
167 168 169 2 100 25 ; GLY(T)-THR(C) SBB
; Sidechain angles
15 16 17 2 150 50 ; PHE
15 16 18 2 150 50 ; PHE
63 64 65 2 180 25 ; LYS
93 94 95 2 150 50 ; PHE
93 94 96 2 150 50 ; PHE
102 103 104 2 150 50 ; HIS
102 103 105 2 150 50 ; HIS
113 114 115 2 180 25 ; LYS
122 123 124 2 180 25 ; LYS
160 161 162 2 180 25 ; LYS
[ dihedrals ]
; Backbone dihedrals
89 90 91 93 1 -120 400 1 ; GLY(1)-ALA(1)-ILE(1)-PHE(1)
90 91 93 97 1 -120 400 1 ; ALA(1)-ILE(1)-PHE(1)-GLN(H)
91 93 97 101 1 -120 400 1 ; ILE(1)-PHE(1)-GLN(H)-ALA(H)
93 97 101 102 1 -120 400 1 ; PHE(1)-GLN(H)-ALA(H)-HIS(2)
97 101 102 106 1 -120 400 1 ; GLN(H)-ALA(H)-HIS(2)-CYS(2)
101 102 106 108 1 -120 400 1 ; ALA(H)-HIS(2)-CYS(2)-ALA(2)
102 106 108 109 1 -120 400 1 ; HIS(2)-CYS(2)-ALA(2)-SER(2)
; Sidechain improper dihedrals
15 17 18 16 2 0 50 ; PHE
93 95 96 94 2 0 50 ; PHE
102 104 105 103 2 0 50 ; HIS
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
2 1 POSRES_FC POSRES_FC POSRES_FC
4 1 POSRES_FC POSRES_FC POSRES_FC
6 1 POSRES_FC POSRES_FC POSRES_FC
8 1 POSRES_FC POSRES_FC POSRES_FC
12 1 POSRES_FC POSRES_FC POSRES_FC
13 1 POSRES_FC POSRES_FC POSRES_FC
15 1 POSRES_FC POSRES_FC POSRES_FC
19 1 POSRES_FC POSRES_FC POSRES_FC
23 1 POSRES_FC POSRES_FC POSRES_FC
27 1 POSRES_FC POSRES_FC POSRES_FC
29 1 POSRES_FC POSRES_FC POSRES_FC
31 1 POSRES_FC POSRES_FC POSRES_FC
33 1 POSRES_FC POSRES_FC POSRES_FC
35 1 POSRES_FC POSRES_FC POSRES_FC
36 1 POSRES_FC POSRES_FC POSRES_FC
40 1 POSRES_FC POSRES_FC POSRES_FC
44 1 POSRES_FC POSRES_FC POSRES_FC
46 1 POSRES_FC POSRES_FC POSRES_FC
48 1 POSRES_FC POSRES_FC POSRES_FC
51 1 POSRES_FC POSRES_FC POSRES_FC
53 1 POSRES_FC POSRES_FC POSRES_FC
55 1 POSRES_FC POSRES_FC POSRES_FC
56 1 POSRES_FC POSRES_FC POSRES_FC
58 1 POSRES_FC POSRES_FC POSRES_FC
61 1 POSRES_FC POSRES_FC POSRES_FC
63 1 POSRES_FC POSRES_FC POSRES_FC
67 1 POSRES_FC POSRES_FC POSRES_FC
71 1 POSRES_FC POSRES_FC POSRES_FC
73 1 POSRES_FC POSRES_FC POSRES_FC
77 1 POSRES_FC POSRES_FC POSRES_FC
79 1 POSRES_FC POSRES_FC POSRES_FC
80 1 POSRES_FC POSRES_FC POSRES_FC
82 1 POSRES_FC POSRES_FC POSRES_FC
85 1 POSRES_FC POSRES_FC POSRES_FC
89 1 POSRES_FC POSRES_FC POSRES_FC
90 1 POSRES_FC POSRES_FC POSRES_FC
91 1 POSRES_FC POSRES_FC POSRES_FC
93 1 POSRES_FC POSRES_FC POSRES_FC
97 1 POSRES_FC POSRES_FC POSRES_FC
101 1 POSRES_FC POSRES_FC POSRES_FC
102 1 POSRES_FC POSRES_FC POSRES_FC
106 1 POSRES_FC POSRES_FC POSRES_FC
108 1 POSRES_FC POSRES_FC POSRES_FC
109 1 POSRES_FC POSRES_FC POSRES_FC
113 1 POSRES_FC POSRES_FC POSRES_FC
117 1 POSRES_FC POSRES_FC POSRES_FC
118 1 POSRES_FC POSRES_FC POSRES_FC
122 1 POSRES_FC POSRES_FC POSRES_FC
126 1 POSRES_FC POSRES_FC POSRES_FC
128 1 POSRES_FC POSRES_FC POSRES_FC
130 1 POSRES_FC POSRES_FC POSRES_FC
132 1 POSRES_FC POSRES_FC POSRES_FC
134 1 POSRES_FC POSRES_FC POSRES_FC
136 1 POSRES_FC POSRES_FC POSRES_FC
137 1 POSRES_FC POSRES_FC POSRES_FC
139 1 POSRES_FC POSRES_FC POSRES_FC
141 1 POSRES_FC POSRES_FC POSRES_FC
142 1 POSRES_FC POSRES_FC POSRES_FC
145 1 POSRES_FC POSRES_FC POSRES_FC
149 1 POSRES_FC POSRES_FC POSRES_FC
150 1 POSRES_FC POSRES_FC POSRES_FC
152 1 POSRES_FC POSRES_FC POSRES_FC
154 1 POSRES_FC POSRES_FC POSRES_FC
156 1 POSRES_FC POSRES_FC POSRES_FC
160 1 POSRES_FC POSRES_FC POSRES_FC
164 1 POSRES_FC POSRES_FC POSRES_FC
165 1 POSRES_FC POSRES_FC POSRES_FC
167 1 POSRES_FC POSRES_FC POSRES_FC
168 1 POSRES_FC POSRES_FC POSRES_FC
#endif
Thank you very much in advance!
P.S I really wanted to upload the water molecules but I can't seem to find a way... if any knows how to upload an image please let me know!
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- Pim
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6 years 3 months ago #7479
by Pim
Replied by Pim on topic My Polarizable Water (PW) beads are bending after EM
Hi Jimmy, thanks for your very clear and well-documented question.
You can see that near the end of your energy minimization the energy goes up steeply (to 10e12), which indeed indicates something is wrong with waters going crazy. Your NVT run therefore immediately explodes. Sadly, even with stiff bonds instead of constraints this sometimes happens. With your systems size, aiming for a max force of 10e3 or 10e4 is normal. The simplest solution that will probably work is simply taking the structure from step 112 or so and continuing with that (if you write every frame with nstxout-compressed=1 you can get it out using trjconv -dump or something like that). However, do also check if these waters are perhaps at the boundaries of your genconf-generated boxes and if the density is homogeneous.
If the above doesn't work, try solvating your system with a different random seed. In some of my self-assembly simulations, I find that in about 10% of the cases I have similar problems and just trying again works. Also, make sure you are using a gromacs version newer than 5.1, gmx solvate had bugs in it. Still even with the latest gmx sometimes I find gmx solvate doesn't always work well for this kind of setups and for some mystery reason you get a box with correct density of water at the edges, but more density in a cube in the middle of the box. You can easily spot this using VMD though. However, with your way of doing it (solvating 1 protein and then using genconf to replicate it), this problem should be minimal. I usually solvate all proteins at the same time (gmx insert-molecules the protein -nmol 48 so they are randomly rotated and then gmx solvate)
Some other tips:
- You never need to do 10,000,000 EM steps. Usually 10,000 is already more than enough.
- You don't have periodic molecules, so don't set that to yes. periodic molecules are molecules that covalently continue on both sides of the box, like infinite polymers or surfaces.
- You probably want to generate some velocities in your NVT start-up (gen_vel yes, otherwise you start at 0 Kelvin)
You can see that near the end of your energy minimization the energy goes up steeply (to 10e12), which indeed indicates something is wrong with waters going crazy. Your NVT run therefore immediately explodes. Sadly, even with stiff bonds instead of constraints this sometimes happens. With your systems size, aiming for a max force of 10e3 or 10e4 is normal. The simplest solution that will probably work is simply taking the structure from step 112 or so and continuing with that (if you write every frame with nstxout-compressed=1 you can get it out using trjconv -dump or something like that). However, do also check if these waters are perhaps at the boundaries of your genconf-generated boxes and if the density is homogeneous.
If the above doesn't work, try solvating your system with a different random seed. In some of my self-assembly simulations, I find that in about 10% of the cases I have similar problems and just trying again works. Also, make sure you are using a gromacs version newer than 5.1, gmx solvate had bugs in it. Still even with the latest gmx sometimes I find gmx solvate doesn't always work well for this kind of setups and for some mystery reason you get a box with correct density of water at the edges, but more density in a cube in the middle of the box. You can easily spot this using VMD though. However, with your way of doing it (solvating 1 protein and then using genconf to replicate it), this problem should be minimal. I usually solvate all proteins at the same time (gmx insert-molecules the protein -nmol 48 so they are randomly rotated and then gmx solvate)
Some other tips:
- You never need to do 10,000,000 EM steps. Usually 10,000 is already more than enough.
- You don't have periodic molecules, so don't set that to yes. periodic molecules are molecules that covalently continue on both sides of the box, like infinite polymers or surfaces.
- You probably want to generate some velocities in your NVT start-up (gen_vel yes, otherwise you start at 0 Kelvin)
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- peterkroon
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6 years 3 months ago #7482
by peterkroon
Replied by peterkroon on topic My Polarizable Water (PW) beads are bending after EM
In addition, did you visually check your protein after the vacuum minimization? If that ran for 10m steps it could produce an unstable conformation.
If what Pim said doesn't help put position restraints on your protein, and equilibrate your solvent (NVT or NPT doesn't matter) with a lower than normal timestep (e.g. 10 fs); or even with the stiff bonds instead of constraints.
If what Pim said doesn't help put position restraints on your protein, and equilibrate your solvent (NVT or NPT doesn't matter) with a lower than normal timestep (e.g. 10 fs); or even with the stiff bonds instead of constraints.
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