[gmx-users] Interchain Disulfide Bond

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 21 01:26:11 CET 2012

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.


> 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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