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

Egidijus Kuprusevicius ekuprusevicius at yahoo.com
Wed Jan 16 12:47:22 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 correctly 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
  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. (it would be in gro let's say 1500 atoms, and in top let's say DGR=1 and SOL=490).
  I know exist some short instructions how to do so, but I couldn't find them in the manual.
  P.S.these links provided are pointing to the empty sites.

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