[gmx-users] Re: converting pdb to gmx successfully

Maik Goette 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
37077 Goettingen
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
> oxygen.
> 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.
> Regards,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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