From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 15 2003 - 13:53:38 CDT
Hi,
There is a new(er) psfgen "regenerate" command to do this:
regenerate [angles] [dihedrals]
Purpose: Remove all angles and/or dihedrals and completely regenerate them
using the segment automatic generation algorithms. This is only needed if
patches were applied that do not correct angles and bonds. Segment and
file defaults are ignored, and angles/dihedrals for the entire molecule
are regenerated from scratch.
Arguments: angles: Enable generation of angles from bonds.
dihedrals: Enable generation of dihedrals from angles.
Context: After one or more segments have been built.
See http://www.ks.uiuc.edu/Research/namd/current/ug/node21.html#2648
-Jim
On Wed, 15 Oct 2003, Andersen, Kim Vilbour (KVA) wrote:
> Dear NAMD users/developers
>
> I have a small problem using the otherwise excellent psfgen tool (it is great for us users that have no access to CHARMm).
>
> I have generated a number of custom residues (glyco residues) and patches to connect them together and to the protein residues.
>
> I can run psfgen and everything works.
>
> BUT my problem is that I have to define all new angles and dihedrals in the PRES definition, whereas I would prefer to use
>
> autogene angles dihed
>
> As it (should) be possible in CHARMm (see e.g. http://www.scripps.edu/brooks/c27docs/struct.html#%20Autogen ).
>
> Unfortunately the autogenerate angles only works during the segment generation, and the patches I apply afterwards needs the angles and dihedrals to be specifically defined :-(
>
> Am I doing anything wrong?
>
> Will the potential to autogenerate angles and dihedrals be incorporated in psfgen at a later stage?
>
> Thanks in advance
>
> Kim V. Andersen
> ------------------------------------------------------------------------
> Kim Vilbour Andersen, PhD
> Senior Scientist
> Maxygen
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> DK-2970 Hørsholm
> Denmark
>
> Tel: +45 7020 5550
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>
> E-mail: kva_at_maxygen.dk
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>
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