[gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS

Egidijus Kuprusevicius ekuprusevicius at yahoo.com
Tue Jan 15 23:34:39 CET 2008

Dear Gromacs developers, I have some very simple questions on how to get the file (tpr) wich could be run on Gromacs (MD). With Hyperhem I have drawn the target molecule, I obtained ent file containing ATOM and CONNECT sections:
  1) What should I change in this ent file to be able to run this file with pdb2gmx (by renaming to pdb) to obtain top and gro? I want to use OPLS ff.
  2) Let's say I have top and gro created using PRODRG server and JML using ffgmx. What I should change in my gro and top or itp (if I choose to create it) to be able to create tpr? I know expicitly all OPLS files like itp (bn and nonbn), atp, rtp, n/c terminals (tdb), hdb. I know how to describe atoms types and bonds for my own molecule, but do not know how to describe dihedrals (proper and unproper)...it looks something like that - C +N O H    impropers_O_C_X_Y ... what does it stand for and what are basic rules for constructing them?
  3) Moreover after creating top and gro using PRODRG server I chose to do everything with gmx ff, but after creating box and solving this molecule in the water I couldn't get tpr file using grompp. I have got the error message that nr of atoms in top(=1500) doesn't match that one in gro(=0). I have tried to follow recomendations in a wiki errors section, but nothing helped me. So why some steps I was able to accompish (it indicates that my cpp on Unix can recognize EOL of Windows) and by runing grompp in order to get tpr I have got this message (I checked the nr in gro and top - both matched)? I have no more ideas what to do.
  I'm using Gromacs3.3
  Thank you in advance

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