Autogene angles dihed / patch / psfgen problem

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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