On 21/02/2012 6:20 AM, jneeraj wrote:
Hello,
I am trying to perform a MD simulation of a protein consisting of two
chains. These two chains are connected via single disulfide bond.
These two chains are separated by TER record in the input pdb file. I am
using charmm27 force-field. The steps that I am following are:
pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -f<PDB> -o<GRO>
-p<TOP>
However this step DOES NOT generate interchain disulfide bond. So, I tried
to generate .top file using:
pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -f<PDB> -o
<GRO> -p<TOP>
When asked for merging chains, I say "y"
-merge and -chainsep do different things. You need separated chains that
are merged into the same moleculetype, because the specbond.dat
mechanism requires that the atoms be in the same [moleculetype]. Check
out pdb2gmx -h and choose a suitable combination of -merge and -chainsep.
The above step generates correct disulfide bonds and termii; however when I
use
I don't think all your termini would be correct, and the subsequent
error suggests that.
Mark
grompp -f min_run.mdp -c<GRO> -p<TOP> –o<TPR>
I get the error:
----------------------------------------
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1346
Fatal error:
Unknown cmap torsion between atoms 3224 3226 3228 3234 3237
----------------------------------------
These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence,
physically this cmap torsion is not required.
I will appreciate your suggestions in helping me resolve this issue.
Thanks,
Neeraj
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