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

[Simone Bolognini]

This was very useful thanks!! Actually I realized that Swiss Pdb Viewer
automatically tries to reconstruct the missing atom positions, so that now
I have the topology.

Thanks a lot!
Simone

Il giorno ven 8 gen 2016 alle ore 00:02 Peter Stern <
peter.stern at weizmann.ac.il> ha scritto:

> 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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