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

[Simone Bolognini]

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