[gmx-users] g_rama/xrama problem in version 3.1.4.

[David]

On Wed, 2003-09-24 at 22:32, istvan at kolossvary.hu wrote:
> Hi, 
> 
> 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, 
> 
> Istvan 
> 
> P.S. Erik had this idea: 
> 
> Hi, 
> 
> 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. 
> 
> Cheers, 
> 
> Erik 
> 
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-- 
David.
________________________________________________________________________
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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