From: Ben Roberts (Ben.P.Roberts_at_vcp.monash.edu.au)
Date: Tue Jul 06 2004 - 00:21:01 CDT
Hi All,
On trying to parametrise proteins etc for NAMD, I have found that it makes
a difference to the energy depending on what order the improper is
specified in the PSF and Parameter files. So:
Atom 1 - Atom 2 (Hub) - Atom 3 - Atom 4
is not the same (from an energy perspective) as
Atom 1 - Atom 2 (Hub) - Atom 4 - Atom 3
etc.
Does anyone know how to choose which atom should be which? I have
gathered that Atom 1 should be the "unique" atom, for instance, the
carbonyl oxygen, or the alkene carbon, or the non-aromatic substituent.
Any advice would be much appreciated.
Thanks in advance and best regards,
Ben
----------------------------------------------------------------------
Benjamin P. Roberts, B.Sc.(Hons)
Ph.D. Student
Department of Medicinal Chemistry
Victorian College of Pharmacy (Monash University)
381 Royal Parade, Parkville VIC 3052, Australia
Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940
----------------------------------------------------------------------
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:44 CST