On Mon, May 9, 2016 at 4:10 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 1* contact maps to get insight about residues important for the assosiation
Check the 'nativecontacts' command of cpptraj.
> 2* electrostatic surface- as the dynamical property of the receptor
> system - to understand whether any differences in it - seen on
> different trajectories which helps me make conclusions regarding
> importance of the electrostatic forces in my system in general.
I believe PBSA has the ability to generate electrostatic potential
density maps which can be visualized by programs like VMD, chimera,
etc.
-Dan
>
> Thanks so much for any help with the realization of those steps using
> different progs from AMBER TOOLS as well as for any extra advises!
>
> James
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 10 2016 - 07:30:03 PDT
