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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 16 13:19:58 CET 2008

Egidijus Kuprusevicius wrote:
> 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.

We being asked about converting .ent formats :-) I think I suggested as 
good a strategy as any. About a minute's googling reveals that Hyperchem 
can write a .pdb format.

>   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

That's a better question. Atom names and residue names need to be 
consistent with what is in the force field files. There are standard 
names for these, and if your PDB-generator uses them then you can feed 
them to pdb2gmx, choose oplsaa and probably do OK. PRODRG is useless 
here. If you need non-standard residues, then see the GROMACS wiki page 
on Parameterization.

>   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)

Chapter 5 in the manual describes the format, chapter 4 describes the 
functions the format defines.

>   '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?).

When replying to someone, please quote their words so that people know 
what you're talking about. I partly remember, because I wrote them, but 
hardly anybody else will.

>   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.

I can't remember what you're talking about here.


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