Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D?
On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani <ankitanaith...@gmail.com> wrote: > Hi, > > I noticed that in my topology file, there is no inclusion of position > restraint file for my protein. For instance, my topology file looks > like this: > > ; Include forcefield parameters > #include "gromos53a6.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_E.itp" > #include "topol_Protein_chain_F.itp" > #include "topol_Protein_chain_G.itp" > > ;Include ligand topology > #include "FDP_Dp.itp" > > ; Include water topology > #include "gromos53a6.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "gromos53a6.ff/ions.itp" > > > But, after running pdb2gmx, I do get 4 posre files for all the > individual chains. Do I need to add in them manually? Also, I am > unable to understand as to why did it not get included in the first > instance itself? I am using gromos53a6 force field. > > > Best Wishes, > > -- > Ankita Naithani -- Ankita Naithani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
