[gmx-users] Running MD on a dimeric protein

Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file in which there were two chain topologies for each chain as : ; Include chain topologies #include topol_A.itp #include topol_B.itp and in Compound section gave ;

Re: [gmx-users] Running MD on a dimeric protein

onetwo wrote: Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file in which there were two chain topologies for each chain as : ; Include chain topologies #include topol_A.itp #include topol_B.itp and in Compound section gave ;

Re: [gmx-users] Running MD on a dimeric protein

The way you define things would work fine but if your dimer is an homodimer only one topology is needed. topol_A and topolo_B should be identical. The part of the mdp file is fine. On Aug 16, 2010, at 7:13 AM, onetwo wrote: Hello Sir, I am simulating a protein which is a homodimer, when I

Re: [gmx-users] Running MD on a dimeric protein

- Original Message - From: onetwo twoon...@rediffmail.com Date: Monday, August 16, 2010 18:55 Subject: [gmx-users] Running MD on a dimeric protein To: gmx-users@gromacs.org Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy

[gmx-users] Running MD on a dimeric protein

Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file in which there were two chain topologies for each chain as : ; Include chain topologies #include topol_A.itp #include topol_B.itp and in Compound section gave ;