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

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 8 09:24:30 CET 2006

> 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

> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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