[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature

[Sandeep Somani]

Hi Anton 

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. 

thnx
sandeep



> -----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.
> 
> 
> -- 
> Groetjes,
> 
> Anton
> 
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> |  _   _  ___,| K. Anton Feenstra                             
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