Re: Protein ligand simulation Tutorial

Date: Wed Feb 29 2012 - 17:01:06 CST

Chris is right - it's not so simple as a "binding free energies"
tutorial that you can follow and then adapt to your complex. There are
considerations of sampling and convergence and method-specific issues,
e.g. definitions of reaction coordinates. These go a bit deeper than
what single tutorials can accomplish.

Please do check the FEP tutorials for one method carry out the free
energy calculation. The choice of calculation method depends on your
system, so it might be worth doing some more literature searches and
come back with a more direct question, so that people can help you

- Poker.

Quoting sai nitin <>:

> Hi all,
> I recently started working on Molecular Dynamics simulation using NAMD I
> wanted to do Protein ligand simulation and compute binding free energies
> can any body suggest any tutorial.
> Thanks in advance
> --
> Sainitin D

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