Re: NAMD Parameter File Creation

From: J T (
Date: Sun Jun 17 2007 - 17:31:27 CDT


I remember seeing this tutorial on the NAMD website. It goes through
the parameterization process using NAMD, VMD and Spartan. You might
have lucked out.



On Jun 17, 2007, at 1:04 PM, Peter Murphy wrote:

> 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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