[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature
ssomani at bii.a-star.edu.sg
Wed Jun 22 10:40:41 CEST 2005
The reason I asked the question was that the atom type (HG) added to the
output .top and .gro file
was not in any of the input parameter files. I made sure to delete
everything except my entries.
so i was wondering if there are any hardcoded atom types in pdb2gmx
which are not picked from the parameter files.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Anton Feenstra
> Sent: Tuesday, June 21, 2005 11:46 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] OPLS, pdb2gmx and hydrogen nomenclature
> Sandeep Somani wrote:
> > Hi
> > As you mentioned I had listed the entries i made to all the
> > parameter files ( ffoplsaa.atp ffoplsaa.rtp ffoplsaanb.itp
> > ffoplsaa.hdb ffoplsaabon.itp ) in my mail. i know the mail was too
> > long!
> > basically my question was --
> > is there is any convention to be followed for
> naming hydrogens
> > in any new molecule ?
> The short answer is: No.
> However, pdb2gmx does follow strict rules for naming
> hydrogens it adds
> according to the hydrogen database (.hdb), see manual for details.
> In addition, for several classes of molecules (e.g.,
> proteins, nucleic
> acids), there are naming conventions.
> * NOTE: New Phone & Fax numbers (below) *
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