Re: [AMBER] Thr -> Met in TI calculation

From: Jason Swails <>
Date: Sat, 5 Jun 2010 09:45:34 -0400


See the amber tutorials . There is a
tutorial, Advanced 9 ( 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!

2010/6/5 fancy2012 <>

> 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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Jun 05 2010 - 07:00:05 PDT
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