[gmx-users] Interchain Disulfide Bond

jneeraj jneeraj at mit.edu
Mon Feb 20 20:12:59 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 solvate.gro -p VAK.top –o min1.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.


View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488594p4488594.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list