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

[Mark Abraham]

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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