AMBER Archive (2009)

Subject: Re: [AMBER] MD snapshots of most probable protein conformations in Amber

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Nov 12 2009 - 07:30:53 CST

I am not sure, but I believe that Andy Mc Cammon's group has implemented
this setup in their own web site, extending it from namd as in the paper
you mentioned, to amber now.

Adrian

Andrew Voronkov wrote:
> Dear Amber users,
> are there any tutorials online on usage of some analogs of relaxed complex scheme, described here:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516539/?tool=pubmed#aff-info
>
> I mean optimization of MD trajectory snapshots and usage of most probable protein conformations from MD trajectories in Amber?
>
>
> Best regards,
> Andrey
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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