Re: AMBER: Targeted MD

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Sat, 08 Sep 2007 18:35:22 -0400

John,
Can you be much more specific as to what you want to do ?
What will be your starting point, and what will you be targeting to ?

Thanks


Beale, John wrote:
> I would like to perform targeted MD on a series of small molecule ligands and their protein receptors. I have created the complete set of files for the ligands with antechamber, and have built the pdb files of the complexes of the ligands bound to the protein sites. It isn't clear to me what to do next. Can someone please give me a stepwise set of instructions that will point me in the right direction? For instance, what additional datasets do I need to perform the targeted MD docking procedures?
>
> Thank you very much!
>
> John
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Sun Sep 09 2007 - 06:07:49 PDT
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