[gmx-users] Generating topology of 3b68.ent

[Simone Bolognini]

Hi Mark,
Thank you for your fast aswer. However, I don't quite get what you mean by
"detective work". What should I exactly look for?
Il 07/gen/2016 19:25, "Mark Abraham" <mark.j.abraham at gmail.com> ha scritto:

> Hi,
>
> It could just be missing from the experimental data. You'll need to do some
> detective work about that pdb entry.
>
> Mark
>
> On Thu, 7 Jan 2016 19:05 Simone Bolognini <simo.bolognini at gmail.com>
> wrote:
>
> > Good evening everyone,
> > I was trying to generate the topology of the ligand binding domain of the
> > human androgen receptor (3B68) with pdb2gmx using
> > pdb2gmx -f 3b68.ent -o ar.gro -p ar.top -ignh
> > using the AMBER-ILDN ff and implict solvent (therefore typing 6 and 6
> again
> > on gromacs v. 4.6.5) and it throws me the following error:
> >
> > Fatal error:
> > Residue 177 named LYS of a molecule in the input file was mapped
> > to an entry in the topology database, but the atom CG used in
> > that entry is not found in the input file. Perhaps your atom
> > and/or residue naming needs to be fixed.
> >
> > What am I doing wrong? You can find the .ent here:
> > http://www.rcsb.org/pdb/explore/explore.do?structureId=3b68
> > Thank you very much for your support!!
> >
> > Simone
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