Re: Protein-ligand simulation

From: Chris Chipot (
Date: Mon Jun 24 2013 - 07:02:24 CDT


a NAMD tutorial for protein-ligand standard binding constant calculations
is currently in alpha-version. It will be tested thoroughly in the
coming days.

If you can wait a little, I should be able to send you a copy by the end of
this week.

Chris Chipot

On 6/24/13 8:51 AM, James Starlight wrote:
> Dear Namd users!
> I'd like to perform simulation of the protein-ligand complex ( In that
> case I'll deal with the water-soluble diffusional ligand). Could you
> provide me with some tutorial for such simulation ? ( in particular
> I'm looking for additional parameters which i should specify in the
> conf files).
> Thanks for help,
> James

Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews                                 Phone: (217) 244-5711
Urbana, Illinois 61801                            Fax:   (217) 244-6078
      It is hard for France to maintain a thirty-five-hour workweek when
      China and India have invented a thirty-five-hour workday.
                                                      Thomas L. Friedman

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