Re: vmd-l: Angles and dihedral generation

From: Jim Phillips (
Date: Sat Sep 02 2006 - 15:25:12 CDT

The most accurate place would be to look at the topology file itself.

My personal advice is to remove the H-H bond from the TIP3 structure and
then run "regenerate angles dihedrals" on the whole structure before you
write it out. This is required if you're using CHARMM 31 or newer
parameter files where the patches no longer include angles and dihedrals.


On Fri, 1 Sep 2006, Cesar Luis Avila wrote:

> Where can I find information on when to generate angles and dihedrals for
> different segments?
> Throughout internet I have found different ways for generating segments
> For water
> {first none
> last none
> auto none }
> According to psfgen manual "Because CHARMM uses an additional H-H bond we
> must disable generation of angles and dihedrals for segments containing
> waters". Does this apply only to TIP3? What about other water models?
> For membranes :
> {first none
> last none
> auto none dihedrals}
> This options were used by membrane builder on VMD. Does this also apply to
> other lipids like DMPC? Why shouldn't angles be generated in this case?
> At last for proteins
> {first nter
> last cter
> auto angles dihedrals}
> This options were used by autopsf builder on VMD.
> Any help will be very much appreciated.
> Regards
> Cesar

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