Re: Re: vmd-l: Angles and dihedral generation

From: Cesar Luis Avila (
Date: Mon Sep 04 2006 - 10:00:35 CDT

I am using CHARMM 27 parameter files included on VMD:

In particular for TIP3 residue there is an explicit indication to
generate with no angle nor dihedral:

"tip3p water model, generate using noangle nodihedral"

For DMPC there is no explicit indication on topology file, so I suppose
that one should generate angles and dihedrals. This also applies for
POPC. So I don't know why membrane builder on VMD uses auto none
dihedrals for lipids segment. Shouldn't it be auto angles dihedrals?
Since dihedrals are generated from angles what is the point of using
such a command?


Jim Phillips escribió:
> 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.
> -Jim
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:32 CST