From: Andersen, Kim Vilbour (KVA) (KVA_at_maxygen.dk)
Date: Wed Oct 15 2003 - 06:27:17 CDT
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
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Kim Vilbour Andersen, PhD
Senior Scientist
Maxygen
Agern Allé 1
DK-2970 Hørsholm
Denmark
Tel: +45 7020 5550
Direct: +45 4517 8473
Mobile: +45 2637 3727
Fax: +45 7020 5530
E-mail: kva_at_maxygen.dk
http://www.maxygen.dk/
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