[gmx-users] Interchain Disulfide Bond

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

[gmx-users] Interchain Disulfide Bond

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 –

[gmx-users] Re: Interchain Disulfide Bond

Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f -o -p $grompp -f -c -p -o and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27 force field instead of amber99sb, I g

[gmx-users] g_rdf -surf -rdf res_com: details needed

Hello, I wish to compute rdf of Na+ ions around protein surface. I use the command: g_rdf -f traj.xtc -n index.ndx -o rdf_prot_Na_res_com.xvg -b 4 -s md.tpr -surf mol -rdf res_com -bin 0.01 Since when -surf option is used, g_rdf does not normalize the rdf, I am curious what does actually g_rdf

[gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

Hello, I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs ver 4.5.5 with charmm27 force-field. Though charmm27 force-field (top_all27_prot_lipid.inp, also see http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm