[gmx-users] generation of proper dihedrals for protons

[Erik Lindahl]

Chris Spronk wrote:
> Hi there,
> 
> I just tried to use the option in pdb2gmx to generate all proper 
> dihedrals involving hydrogens (option -alldih). The option is still 
> described in the manual but apparantly not available anymore in the 
> 3.1.4 distribution. Does anyone have an older version of pdb2gmx that I 
> could try to use for this purpose, or are there other ways to generate 
> all proper dihedrals for protons.
> 

Hi Chris,

If you look at the top of the residue topology file ffoplsaa.rtp, 
there's an option to generate all dihedrals. You could just edit the 
ffgmx.rtp file (or G96) and have it generate all dihedrals.

Cheers,

Erik