[gmx-users] multiple dihedral function types - regd

Mark Abraham 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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