VMD-L Mailing List

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Mon Jun 21 2010 - 18:09:28 CDT

If you want to use amber ff. topologies and parameters within a charmm
psf format for a namd simulation, you can use psfgen
to generate a psf file. You just have to look for the amber ff
topologies and parameters that have been converted into a charm topology
and parameters format.

Check this link here:
http://terpconnect.umd.edu/~jbklauda/research/download.html

Usually, if you want to run a simulation using amber ff in namd, just
use ambertools to generate the parmtop file and check out the namd
manual on what settings you have to make to use the ff correctly.

George 

-- 
________________________________________________________________________
George Madalin Giambasu                        PhD Student
University of Minnesota                        Phone : (612) 625-6317
Department of Chemistry                        Fax   : (612) 626-7541
207 Pleasant St. SE                            e-mail:
Minneapolis, MN USA 55455-0431                 GeorgeMGiambasu_at_umn.edu
York Research Group                            giambasu_at_gmail.com
http://theory.chem.umn.edu/~giambasu
________________________________________________________________________