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

Erik Lindahl lindahl at csb.stanford.edu
Wed Sep 24 22:47:00 CEST 2003

Hi David,

> 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.

I haven't had any time to look at the code, but do you remember if we 
use atom names to detect the dihedrals, or?

(Note that the problematic dihedral in this case involved an N-terminal 
ACE cap - that might cause it).

The OPLS phi/psi dihedrals should be defined in the same way as 
Gromos/Gromacs, but they are of type 3 instead of type 1.

Istvan: Try it using OPLS with the ALA-ALA dipeptide I suggested - if 
that works it is just due to the ACE cap (probably atom names), if not 
it is the forcefiels (probably dihedral type definitions).



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