VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jun 30 2005 - 10:40:34 CDT

Most residues in the topology file don't list angles and dihedrals, so
they are automatically generated based on the bonds. There is a line near
the top of the topology file that specifies this. Impropers are always
listed. You use "auto none" for the exceptions, especially water.

-Jim

On Wed, 29 Jun 2005, vivek sharma wrote:

> Hello all,
>
> Please explain me the concept of auto none in psfgen.
>
> As per documentation of psfgen, when I dont use 'auto none' in 'segment'
> command, it generates all angles and dihedrals automatically. what does
> this mean? Does it mean that all angles and dihedrals are generated
> automatically (by some means) by psfgen without using the angle and
> dihedral entries of residues in topology file?
>
> Any comments will be helpful.
>
> Thanks in advance,
>
> Regards,
>
> VIvek
>
> --
> VIVEK SHARMA
> HBG BI
> "Basic research is what I'm doing when I don't know what I'm doing."
> - Werner von Braun
>