[gmx-users] multiple dihedral function types - regd
Mark.Abraham at anu.edu.au
Wed Apr 11 04:39:53 CEST 2012
On 11/04/2012 3:33 AM, ramesh cheerla wrote:
> Dear gromacs users,
> For one of my residues i have two types
> of dihedral functions, i.e C-C dihedrals are in periodic type and
> C-O dihedrals are in the Ryckaert-bellemans type, now i want to
> generate the topology file for this residue is it possible to use the
> two dihedral function types for this residue. I have tried by using
> two different dihedraltypes directives one is for the periodic type
> and another one is for Ryckaert-Bellemans function, but how can i
> incorporate the two functional types in the dihedrals section of the
> bondedtypes directive in aminoacids.rtp.
You can't. That is a limitation of pdb2gmx.
> or is there any methods in gromacs to convert one dihedral functional
> form to the other.
Basic trig will let you express a periodic dihedral of sufficiently
small periodicity in R-B form. However that's only a reasonable solution
with pdb2gmx if the force field uses only R-B dihedrals.
It may be more effective to use pdb2gmx and to replace the inappropriate
dihedral form in the .top file by hand afterwards.
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