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" The above step generates correct disulfide bonds and termii; however when I use 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 -- View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488616p4488616.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
