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

[Peter Stern]

Look for any "MISSING ATOMS" in the pdb file (in the REMARKS).
Look at the coordinates given for the LYS in question and check if there are coordinates for the CG.

Experimental data isn't "perfect."  PDB entries have missing residues and missing atoms all the time because they couldn't be resolved.

"Detective work" is over-glamorizing it.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Simone Bolognini
Sent: Thursday, January 07, 2016 8:37 PM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Generating topology of 3b68.ent

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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