NAMD Parameter File Creation

From: Peter Murphy (murffyp_at_gmail.com)
Date: Sun Jun 17 2007 - 12:04:51 CDT

Hi everyone, I just had a quick question regarding creation of a parameter
file to create a PSF-PDB combo. I am trying to create a parameter file for
UDP-GlcNAc (UDP-N-acetylglucosamine) so I can create a PDB-PSF combo to be
used in an NAMD simulation. I don't have access to AMBER, but I do have
accesses to SPARTAN (a quantum mechanical modeler).

I have done google searches as well as a quick search of the NAMD-L mailing
list achieve but have yet been able to create the parameter file.

I've read many places about creating a parameter file based on chunks of
other molecules (which have parameters) but nothing really explains in
enough detail how to do this...

Anyone have some ideas.. anything would be greatly appreciated...

Peter

-- 
Peter Murphy, B.Sc., M.Sc Candidate,
Vice President (Graduate), Dalhousie Biochemistry Students Society
Atlantic Research Centre
Dalhousie University
Halifax, Nova Scotia,
Canada

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