[gmx-users] g_rama/xrama problem in version 3.1.4.
spoel at xray.bmc.uu.se
Wed Sep 24 22:41:02 CEST 2003
On Wed, 2003-09-24 at 22:32, istvan at kolossvary.hu wrote:
> I ran a 1ns md on ACE-ALA-NAC (sometimes called alanine dipeptide) and
> wanted to look at the Ramachandran plot. Both g_rama and xrama abort after
> finding the correct number of a single phi-psi pair. A fatal error message
> comes from nrama.c that reads something like "Dihedral about 6,8 cannot be
> found in topology". "6" is a C=O oxygen of ACE and "8" is a NH hydrogen of
> ALA, there shouldn't be any dihedral between them, should it. I guess the
> topology should be fine since I can run a whole simulation with it. I wonder
> if this has something to do with the same problem that I posted yesterday
> (atomtype mismatch in the .rtp and .hdb files for NAC). Can you give me a
> hint. I am kind of discouraged since I am doing very simple things.
> Many thanks,
> P.S. Erik had this idea:
> Ah, I'm almost positive it's just a problem in the analysis code.
> I didn't write the core of g_rama myself, so you might want to post it to
> the mailing list where Berk & David read things too.
I suspect it's a force field problem, that is you used OPLS, whereas I'm
afraid to admit that part of this code expects the topology to have
gromos-like dihedrals. If this is the case you coud remake a topology
using the ffgmx2 force field and use that for this analysis only.
> ACE-ALA-NAC isn't a dipeptive, but a capped single amino acid. g_rama
> detects phi/psi dihedrals automatically, and the original gromacs/gromos87
> forcefields didn't use caps a lot, so my guess would be that the automatic
> code to find the phi/psi dihedrals based on atom names fails.
> Try it with a normal terminated (NH3+ and COO-) ALA-ALA and see if that
> works. If it does, it is just the detection code in g_rama that needs to be
> updated; you might even want to have a look, it's a fairly small program.
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David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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