[gmx-users] Interchain Disulfide Bond

jneeraj jneeraj at mit.edu
Mon Feb 20 20:20:33 CET 2012


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" 

The above step generates correct disulfide bonds and termii; however when I

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. 


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