[gmx-users] Error in protonating ASP in pdb2gmx.

Marcin Wojciechowski nitramus at hypnos.chem.pg.gda.pl
Thu Dec 5 15:23:31 CET 2002

> >>"Fatal error: Atom HD1 not found in rtp database in residue ASPH,
> >>it looks a bit like HD2"
> >>
> >>There exist only HD2 in rtp. Why pdb2gmx don't use this one
> > 
> > 
> > You can just change the OD1 to OD2 and vice versa and name
the HD1 HD2
> > in the pdb file
> It sounds like a bug in the .hdb file.

and indeed it's a bug. In .hdb file I found an entry for [ ASPH ]
regarding atom OD1. After changing it to OD2, pdb2gmx added HD2 to ASP's
and there was no complains.

BUT: I discovered another BUG in the ffgmx2.rtp file. Grompp was
complaining about [ GLUH ] impropers. So I checked the entries in .rtp
file and in the [ bonds ] section of [ GLUH ] there is  "CB     C". If "C"
is the carbonyl carbon then CB should be changed to CA. So after the
chnges everything is fine now.

Best regards, Martin.

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