[gmx-users] FEP

[Justin A. Lemkul]

Steven Neumann wrote:
> Thank you guys! So, is there any tutorial in Gromacs for calculating 
> free energy of ligand binding using FEP?
>  

TI or BAR are better methods for calculating binding free energies, I would 
think.  FEP is best for mutating between different species.

-Justin

> Steven
> 
> On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     mohsen ramezanpour wrote:
> 
>         Hi
>         Please have a look at Dr.Justin tutorial page at the following link:
> 
>         http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/index.html
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html>
> 
> 
>     This tutorial is not for FEP explicitly, but may be of some use.
>      There is discussion on using the BAR algorithm for binding free
>     energy calculations.
> 
>     -Justin
> 
>         Cheers
> 
> 
>         On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann
>         <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>__>
>         wrote:
> 
>            Hi Gmx Users,
>                 Can you suggest some reading and some tutorial in
>         calculations of
>            binding free energy (ligand binding) in Gromacs? ?I want to
>         use Free
>            Energy Perturbation method.
>                 Steven
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> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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