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 -- 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
