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

[David Mathog]

> > 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