normal martini script

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6 years 6 months ago #1244 by nivedita
martini script was created by nivedita
Dear All,
I am trying to do coarse grained simulation for simple protein in water .I used Gromacs 4.5.4 version ( in ubunto 12.0) for cg 100ns simulation then i extract last frame and for reverse transformation so for that i install gromacs 3.3.1 in cygwin (in Windows7).
then i need fg.top file so what i did is that, take original pdb structure
pdb2gmx -f original.pdb -p fg.top -missing
then i choose GROMOS43a1 force field , it generate conf.gro ,posre.itp and fg.top file
editconf
genbox
grompp
genion
for adding ions
grompp for minimization
then i used final fg.top having ,
Protein 1
SOL 30179
CL- 2
and manipulate fg.top by replacing spce.itp by ; Include water topology
#include "fg_w.itp" and SOL 30179 by FG_W 6526 because cg .top file has W 6526.
then i used this manipulated fg.top file for reverse transformation ,

g_fg2cg -pfg fg.top -pcg system.top -c last_frame.pdb -n 0 -o fg.gro
it shows following error
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 0 bonded neighbours for FG_W 6526
Excluding 1 bonded neighbours for CL- 2
# G96BONDS: 4095
# HARMONIC: 26104
# G96ANGLES: 5929
# PDIHS: 2283
# IDIHS: 1834
# LJ14: 7051
# CONSTR: 78312
calling cpp...
processing topology...
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for W 6526
Excluding 1 bonded neighbours for CL- 2

Number of fg atoms 82371
Number of cg atoms 7395
Reading frame 0 time 100000.000 1352041772
Name of CG water in topology should be W
Segmentation fault (core dumped)

but when i ignore system.top (i.e. for cg topology )file then it generate fg.gro file
g_fg2cg -pfg topol.top -c last_frame.pdb -n 0 -o fg.gro
then it shows
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 0 bonded neighbours for FG_W 6526
Excluding 1 bonded neighbours for CL- 2
# G96BONDS: 4095
# HARMONIC: 26104
# G96ANGLES: 5929
# PDIHS: 2283
# IDIHS: 1834
# LJ14: 7051
# CONSTR: 78312
calling cpp...
cpp: topol.top: No such file or directory
cpp: warning: '-x c' after last input file has no effect
cpp: no input files
cpp exit code: 256
Tried to execute: 'cpp -I/usr/local/gromacs/share/gromacs/top topol.top > grom ppUahhu7'
The 'cpp' command is defined in the .mdp file
processing topology...

Number of fg atoms 82371
Number of cg atoms 0
Reading frame 0 time 100000.000 1352042419
Name of CG water in topology should be W

Fg pre-structure computed !
then follow further steps
grompp -f fg.mdp -c fg.gro -p fg.top -o topol.tpr
it showing error
creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable coulombtype, using 'Cut-off'ield
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field' 'P ME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born' 'Reactio n-Field-nec' 'Encad-shift' 'PME-User'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 'Andersen- interval'
' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
' for variable rel_water, using 'no'
Next time use one of: 'no' 'yes'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
...ling /lib/cpp
: No such file or directory
cpp exit code: 32512
-I/usr/local/gromacs/share/gromacs/top topology.top > gromppvfo9RR'
' command is defined in the .mdp file
processing topology...
processing coordinates...
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 443

Fatal error:
number of coordinates in coordinate file (fg.gro, 82371)
does not match topology (fg.top, 0)

it is bcoz i manipulate fg.top file.

will you please tell me the right way to do this? and where i did mistake? and which step i have to skip?

Thanks in advance

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6 years 6 months ago #1246 by djurre
Replied by djurre on topic martini script
Yes, there is something wrong with you top file. I can't say what if I can't see what is in the .top file. Copy-paste the content here.

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6 years 6 months ago #1251 by nivedita
Replied by nivedita on topic martini script
hello Djurre,
my topol.top having all-atom topology file

; Include forcefield parameters
#include "ffG43a1.itp"

[ moleculetype ]
; Name nrexcl
Protein 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NL 1 GLN N 1 0.129 14.0067 ; qtot 0.129
2 H 1 GLN H1 1 0.248 1.008 ; qtot 0.377
3 H 1 GLN H2 1 0.248 1.008 ; qtot 0.625
4 H 1 GLN H3 1 0.248 1.008 ; qtot 0.873
5 CH1 1 GLN CA 1 0.127 13.019 ; qtot 1
6 CH2 1 GLN CB 2 0 14.027 ; qtot 1......................so on
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2 ................
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1...............
[ mapping ]
;mapping for multiscale simulations
1 1 2 3 4 5 13 14
2 6 7 8 9 10 11 12....................
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 2 ga_9..........................
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 13 1 gd_14
1 5 6 7 1 gd_17.....................
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 1 13 6 2 gi_2
7 10 9 8 2 gi_1...........................
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "fg_w.itp" *here i change spc.itp by fg_w.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein 1
FG_W 6526 *here i change SOL 30179 by FG_W 6526
CL- 2

system.top is,
#include "./martini_v2.2.itp"
#include "./martini_v2.0_ions.itp"

#include "Protein.itp"

[ system ]
; name
Martini system from monomer.pdb

[ molecules ]
; name number
Protein 1
W 6526
CL- 2

one more doubt i have ,
(1)in all atom topology file (topol.top) how SOL/FG_W having 3 atoms in each water molecule become equal to cg water (1 residue having 1 atom) ?
(2)when im working in gromacs 3.3.1 version for complete simulation from starting then first script ./martinize.py -f file.pdb -x cg.pdb -ss file.dssp -p backbone
it do not generate Protein.itp but when i change the martinize.py version 2.1 latest one then it run till minimization but when i run for NVT it says nvt.xtc cannot open
same nvt.mdp parameter what i gave in gromacs 4.5.4 for 100ns simulation is not working here.

please suggest me what i have to do?

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6 years 6 months ago #1253 by xavier
Replied by xavier on topic martini script
It is not clear what goes wrong in your system, but it seems that the conversion CG-AA is not optimal. This appears from the water already.

You may want to get things sorted and make them a bit more clear for us to be able to help you.

XAvier.

nivedita wrote: hello Djurre,
my topol.top having all-atom topology file

; Include forcefield parameters
#include "ffG43a1.itp"

[ moleculetype ]
; Name nrexcl
Protein 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NL 1 GLN N 1 0.129 14.0067 ; qtot 0.129
2 H 1 GLN H1 1 0.248 1.008 ; qtot 0.377
3 H 1 GLN H2 1 0.248 1.008 ; qtot 0.625
4 H 1 GLN H3 1 0.248 1.008 ; qtot 0.873
5 CH1 1 GLN CA 1 0.127 13.019 ; qtot 1
6 CH2 1 GLN CB 2 0 14.027 ; qtot 1......................so on
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2 ................
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1...............
[ mapping ]
;mapping for multiscale simulations
1 1 2 3 4 5 13 14
2 6 7 8 9 10 11 12....................
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 2 ga_9..........................
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 13 1 gd_14
1 5 6 7 1 gd_17.....................
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 1 13 6 2 gi_2
7 10 9 8 2 gi_1...........................
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "fg_w.itp" *here i change spc.itp by fg_w.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein 1
FG_W 6526 *here i change SOL 30179 by FG_W 6526
CL- 2

system.top is,
#include "./martini_v2.2.itp"
#include "./martini_v2.0_ions.itp"

#include "Protein.itp"

[ system ]
; name
Martini system from monomer.pdb

[ molecules ]
; name number
Protein 1
W 6526
CL- 2

one more doubt i have ,
(1)in all atom topology file (topol.top) how SOL/FG_W having 3 atoms in each water molecule become equal to cg water (1 residue having 1 atom) ?
(2)when im working in gromacs 3.3.1 version for complete simulation from starting then first script ./martinize.py -f file.pdb -x cg.pdb -ss file.dssp -p backbone
it do not generate Protein.itp but when i change the martinize.py version 2.1 latest one then it run till minimization but when i run for NVT it says nvt.xtc cannot open
same nvt.mdp parameter what i gave in gromacs 4.5.4 for 100ns simulation is not working here.

please suggest me what i have to do?

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7 months 2 days ago #7869 by riccardo
Replied by riccardo on topic martini script
Never seen this error message:

"A coordinate in file nvt.gro does not contain a '.' "

and I do not understand it at a first glance... but did you check your nvt.gro? I guess the answer to your problem will be there.

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7 months 1 day ago #7873 by riccardo
Replied by riccardo on topic martini script
I have a bit of difficulty to understand what your system is composed of and thus what you want to fill the box with.

In any case, what you want to do sounds pretty basic and the "gmx insert-molecules" and "gmx solvate" commands are what you are looking for. I would recommend following some of the tutorials you find on this website (or some GROMACS tutorial in general) which are full of useful commands lines to create boxes, insert molecules, solvate, etc..

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7 months 1 day ago #7880 by riccardo
Replied by riccardo on topic martini script
*What* do you want to fill the box with? Do you want to have a PEO molecule and solvent or multiple PEO molecules?

Also, please do not spam other threads with the same post like you did in this other thread:

www.cgmartini.nl/index.php/component/kun...bration-problem#7877

thank you.

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7 months 23 hours ago - 7 months 23 hours ago #7882 by riccardo
Replied by riccardo on topic martini script
I understand. Then the "?.gro" in your previous post should be the "npt.gro", which is a single energy-minimized and equilibrated PEO chain. Depending on the length of that chain, you may need a lot of space in the box to fit the 700 chains (the longer they are, the more likely it is that the stochastic placement of molecules of gmx insert-molecules will end up with rejected placements due to overlap of molecules). So, if gmx insert-molecules does not manage to insert all the 700 chains you want in a 20x20x20 box, you can increase the size of the box iteratively (say, 700 chains on 25x25x25, then in a 30x30x30 box etc.) till they fit. You may then end up with a very low density box which needs some "squeezing" (run with a pressure higher than 1 bar) before going on with the melting phase.
Hope this helps.

p.s. Something which could help is also using the "-try" flag of gmx insert molecules (e.g., -try 200) but don't increase that too much otherwise gmx insert-molecules will be stuck for hours trying to fit the same molecules multiple times in a box where there's no hope one more chain is ever gonna fit..
Last edit: 7 months 23 hours ago by riccardo.

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