[gmx-users] Re: gmx-users Digest, Vol 45, Issue 60

Egidijus Kuprusevicius ekuprusevicius at yahoo.com
Wed Jan 16 03:31:55 CET 2008

Thanks Mark,
  but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be understandable to Gromacs.
  I know that PRODGR is not compatible with OPLS, that's why I am asking how to change gro and top to enable them to be compatible with OPLS
  The same story and with beta files (with ff43a1.itp)
  I'm trying to run MD using OPLS with my own molecule solved in the water, for that I was trying to create mymolecule.itp database file, and in order to do so I need to know how to describe corectly dihedrals (in OPLS standart)
  what indicates? it's just simple logic if I use edited on Windows files to produce new gro and updated top files on Unix, that indicates to me that cpp have no errors in reading these files (may be I am wrong, because I do not know how these files are processed during each of these precesses - like genbox and editconf, probably it's different from grompp?).
  number of molecules of whater in top x3+1(my molecule)xn(number of atoms in that molec.)=total nr of atoms in gro file

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