[gmx-users] multiple dihedral function types - regd

ramesh cheerla rameshgromacs at gmail.com
Wed Apr 11 05:57:09 CEST 2012

Thank you mark.

On Wed, Apr 11, 2012 at 8:09 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
> Mark
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