[gmx-users] Re: converting pdb to gmx successfully
mgoette at mpi-bpc.mpg.de
Thu Feb 9 12:35:01 CET 2006
You can add the missing terminal oxygen via ADDOXT in WHATIF
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David Mathog wrote:
>>>Ideally it would be nice if pdb2gmx could generate the N and C termini
>>>all by itself. It looks like "all" that's needed for that are -n.tdb
>>>and -c.tdb files. However I don't know yet how to write those. Does
>>>anybody have these already for the Amber FF files?
>>Amber has completely different residues for the termini, you will have
>>to rename your terminal residues to the special AMber C or N versions,
>>for e.g. ALA you need either CALA or NALA
> I have code to handle that already. The problem is that if I force
> the names by using the chain termini positions pdb2gmx blows up
> later when it finds the missing N Hydrogens and C carboxyl oxygen.
> So those atoms need to be present in the PDB file (or have been added to
> it by pdb2gmx) before the Amber names are applied. At this point I can
> get the hydrogens from whatif output, but no source yet for the carboxyl
> The handling of CYS is also a bit of a problem. pdb2gmx keeps changing
> that name back and forth CYS<->CYSH and doing stuff in between. That
> code just isn't compatible with other naming conventions.
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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