Hello,
See the amber tutorials
http://ambermd.org/tutorials/ . There is a
tutorial, Advanced 9 (
http://ambermd.org/tutorials/advanced/tutorial9/) that
specifically deals with setting up (and running!) TI simulations to use soft
core potentials. Both the manual and these tutorials can offer a great deal
more instruction and advice than any response on a mailing list can, so it
would probably be a good idea to check those sources first before consulting
the list.
Good luck!
Jason
2010/6/5 fancy2012 <fancy2012.yeah.net>
> Dear amber users,
>
> I want to calculate the relative binding free energy between a small
> molecule binding to a protein of Wild Type and Thr -> Met using TI, so how
> should I prepare the two topology files of the protein (both WT and Thr ->
> Met)? Any suggestions will be highly appreciated?
>
> All the best,
> fancy
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jun 05 2010 - 07:00:05 PDT
