- Posts: 18
MARTINI Coarse-Grained DNA-martinize-dna.py
- doa.hawamdeh
-
Topic Author
- Offline
- Fresh Boarder
Less
More
9 years 2 months ago #4453
by doa.hawamdeh
MARTINI Coarse-Grained DNA-martinize-dna.py was created by doa.hawamdeh
Hello,
I tried to use martinize-dna.py script to create the topologies for dsDNA molecules:
python martinize-dna.py -dnatype ds -f [input.gro] -o [topology.top] -x [cg-dna.pdb].
then I used the script editconf to convert the .pdb file into .gro file in order to use it as an input file for grompp processor in GROMACS.
But in the simulation the DNA molecule solvated in water was not OK and I got segmentation fault!!! the .mdp file was good I think the problem is in the topology!!
Please can anyone help me??
Thanks
Doa
I tried to use martinize-dna.py script to create the topologies for dsDNA molecules:
python martinize-dna.py -dnatype ds -f [input.gro] -o [topology.top] -x [cg-dna.pdb].
then I used the script editconf to convert the .pdb file into .gro file in order to use it as an input file for grompp processor in GROMACS.
But in the simulation the DNA molecule solvated in water was not OK and I got segmentation fault!!! the .mdp file was good I think the problem is in the topology!!
Please can anyone help me??
Thanks
Doa
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
9 years 2 months ago #4454
by jaakko
Replied by jaakko on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Doa,
did you use the mdp file that comes in the DNA beta package? DNA requires quite a bit shorter time step than Martini lipids for example so you need to adjust the mdp file accordingly.
If your simulation crashes even with the provided mdp file please send the appropriate lines from your mdp file, your mdrun command you used to start the simulation and the output of mdrun with the error message.
- Jaakko
did you use the mdp file that comes in the DNA beta package? DNA requires quite a bit shorter time step than Martini lipids for example so you need to adjust the mdp file accordingly.
If your simulation crashes even with the provided mdp file please send the appropriate lines from your mdp file, your mdrun command you used to start the simulation and the output of mdrun with the error message.
- Jaakko
Please Log in or Create an account to join the conversation.
- doa.hawamdeh
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 18
9 years 2 months ago #4456
by doa.hawamdeh
Replied by doa.hawamdeh on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hello,
Yes I used the .mdp file in the DNA beta package.
mdp file:
integrator = md
dt = 0.010
nsteps = 50000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 320
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
mdrun command:
grompp -f example.mdp -c 4NZX-solvated-EM.gro -p 4NZX.top -o 4NZX-eq.tpr
mdrun -v -deffnm 4NZX-eq -rdd 1.8
The output:
50000 steps, 500.0 ps.
step 0
Step 6, time 0.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.126241, max 0.198854 (between atoms 120 and 117)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 46.0 0.2290 0.2584 0.2290
120 117 74.4 0.1621 0.1942 0.1620
Step 6, time 0.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.026248, max 0.128564 (between atoms 117 and 118)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 46.0 0.2290 0.2584 0.2290
120 117 74.4 0.1621 0.1942 0.1620
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 646.725599, max 3087.056396 (between atoms 117 and 118)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 88.7 0.2584 707.1650 0.2290
120 117 87.9 0.1942 764.6729 0.1620
118 120 89.1 0.3242 232.0064 0.3250
Back Off! I just backed up step7b_n6.pdb to ./#step7b_n6.pdb.2#
Back Off! I just backed up step7c_n6.pdb to ./#step7c_n6.pdb.2#
Wrote pdb files with previous and current coordinates
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 3030.177003, max 4719.203125 (between atoms 120 and 117)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 88.7 0.2584 707.1650 0.2290
120 117 87.9 0.1942 764.6729 0.1620
118 120 89.1 0.3242 232.0064 0.3250
125 126 103.8 0.3220 37.0162 0.3220
124 125 90.0 0.2170 186.7309 0.2170
126 124 90.1 0.2650 187.4608 0.2650
Back Off! I just backed up step7b_n3.pdb to ./#step7b_n3.pdb.2#
Back Off! I just backed up step7c_n3.pdb to ./#step7c_n3.pdb.2#
Wrote pdb files with previous and current coordinates
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 376.971425, max 859.510986 (between atoms 124 and 125)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
124 125 90.0 0.2170 186.7309 0.2170
126 124 90.1 0.2650 187.4608 0.2650
125 126 103.8 0.3220 37.0162 0.3220
Back Off! I just backed up step7b_n2.pdb to ./#step7b_n2.pdb.2#
Back Off! I just backed up step7c_n2.pdb to ./#step7c_n2.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault
Thank you for reply
Doa
Yes I used the .mdp file in the DNA beta package.
mdp file:
integrator = md
dt = 0.010
nsteps = 50000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 320
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
mdrun command:
grompp -f example.mdp -c 4NZX-solvated-EM.gro -p 4NZX.top -o 4NZX-eq.tpr
mdrun -v -deffnm 4NZX-eq -rdd 1.8
The output:
50000 steps, 500.0 ps.
step 0
Step 6, time 0.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.126241, max 0.198854 (between atoms 120 and 117)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 46.0 0.2290 0.2584 0.2290
120 117 74.4 0.1621 0.1942 0.1620
Step 6, time 0.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.026248, max 0.128564 (between atoms 117 and 118)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 46.0 0.2290 0.2584 0.2290
120 117 74.4 0.1621 0.1942 0.1620
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 646.725599, max 3087.056396 (between atoms 117 and 118)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 88.7 0.2584 707.1650 0.2290
120 117 87.9 0.1942 764.6729 0.1620
118 120 89.1 0.3242 232.0064 0.3250
Back Off! I just backed up step7b_n6.pdb to ./#step7b_n6.pdb.2#
Back Off! I just backed up step7c_n6.pdb to ./#step7c_n6.pdb.2#
Wrote pdb files with previous and current coordinates
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 3030.177003, max 4719.203125 (between atoms 120 and 117)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
117 118 88.7 0.2584 707.1650 0.2290
120 117 87.9 0.1942 764.6729 0.1620
118 120 89.1 0.3242 232.0064 0.3250
125 126 103.8 0.3220 37.0162 0.3220
124 125 90.0 0.2170 186.7309 0.2170
126 124 90.1 0.2650 187.4608 0.2650
Back Off! I just backed up step7b_n3.pdb to ./#step7b_n3.pdb.2#
Back Off! I just backed up step7c_n3.pdb to ./#step7c_n3.pdb.2#
Wrote pdb files with previous and current coordinates
Step 7, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 376.971425, max 859.510986 (between atoms 124 and 125)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
124 125 90.0 0.2170 186.7309 0.2170
126 124 90.1 0.2650 187.4608 0.2650
125 126 103.8 0.3220 37.0162 0.3220
Back Off! I just backed up step7b_n2.pdb to ./#step7b_n2.pdb.2#
Back Off! I just backed up step7c_n2.pdb to ./#step7c_n2.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault
Thank you for reply
Doa
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
9 years 2 months ago #4458
by jaakko
Replied by jaakko on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Doa,
Ok, I had a look at the pdb structure you're studying. You will have to modify the elastic network to simulate that. If you've just run it through martinize I'd expect the elastic network to be completely messed up for at least the last two chains (the ds-soft/ds-stiff options assume there are just two chains in the gro file). A first guess would be to split it into those two separate double helices and run them separately through martinize. If all of them are supposed to be hybridized in some parts you'll have to tweak the elastic network even more than that. But all those details depend on what exactly you're studying here.
- Jaakko
Ok, I had a look at the pdb structure you're studying. You will have to modify the elastic network to simulate that. If you've just run it through martinize I'd expect the elastic network to be completely messed up for at least the last two chains (the ds-soft/ds-stiff options assume there are just two chains in the gro file). A first guess would be to split it into those two separate double helices and run them separately through martinize. If all of them are supposed to be hybridized in some parts you'll have to tweak the elastic network even more than that. But all those details depend on what exactly you're studying here.
- Jaakko
Please Log in or Create an account to join the conversation.
- doa.hawamdeh
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 18
9 years 2 months ago #4459
by doa.hawamdeh
Replied by doa.hawamdeh on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Jaakko,
I want to study the interaction between the double stranded DNA and PAMAM dendrimer in water(solvent). Please, how can I modify the elastic network? and how can I split the dsDNA into two seperate chains?
Doa
I want to study the interaction between the double stranded DNA and PAMAM dendrimer in water(solvent). Please, how can I modify the elastic network? and how can I split the dsDNA into two seperate chains?
Doa
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
9 years 2 months ago #4460
by jaakko
Replied by jaakko on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Doa,
if you want to study a dsDNA with a dendrimer there should be no problems. But the pdb structure you mentioned (4NZX) has four chains (two double-stranded DNAs). Modify the input gro file so that there's only a single dsDNA there and it should work fine.
- Jaakko
if you want to study a dsDNA with a dendrimer there should be no problems. But the pdb structure you mentioned (4NZX) has four chains (two double-stranded DNAs). Modify the input gro file so that there's only a single dsDNA there and it should work fine.
- Jaakko
Please Log in or Create an account to join the conversation.
- doa.hawamdeh
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 18
9 years 2 months ago #4465
by doa.hawamdeh
Replied by doa.hawamdeh on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Jaakko,
Thank you...
I tried to use one chain of the DNA, it worked fine when I ran the DNA alone, but with dendrimer I got warning said that I have a problem with the boundary conditions (cannot fix pbc) and the .gro file has nan values !!!
Please, What shall I do??!!!
Thanks
Doa
Thank you...
I tried to use one chain of the DNA, it worked fine when I ran the DNA alone, but with dendrimer I got warning said that I have a problem with the boundary conditions (cannot fix pbc) and the .gro file has nan values !!!
Please, What shall I do??!!!
Thanks
Doa
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
9 years 2 months ago #4472
by jaakko
Replied by jaakko on topic MARTINI Coarse-Grained DNA-martinize-dna.py
Hi Doa,
there isn't enough information to say much but check step-wise where your gro file breaks. Make sure it's okay after you've coarse-grained your dendrimer and DNA. Then check the gro file after energy minimization and so forth.
- Jaakko
there isn't enough information to say much but check step-wise where your gro file breaks. Make sure it's okay after you've coarse-grained your dendrimer and DNA. Then check the gro file after energy minimization and so forth.
- Jaakko
Please Log in or Create an account to join the conversation.
Time to create page: 0.101 seconds