Re: how to do: FEP e2?, a protonating mutation?

From: Sébastien Légaré (Sebastien.Legare_at_rsvs.ulaval.ca)
Date: Wed Apr 15 2009 - 22:32:27 CDT

Hi Sebastian

Thank you very much.

Do you mean I should raise the barrier with λ, and lower it in the backward
simulations? I meant to raise it from the beginning and let it raised for all
the simulation. Can we change bonded parameters during FEP in NAMD? I am
still using version 2.6 right now.

Sébastien

On April 15, 2009 10:54:58 pm you wrote:
> Hi Sébastien,
>
> > Is it safe to say that raising this barrier does not affect the computed
> > free energy otherwise than by ensuring a syn conformation?
>
> I believe so, as long as the barrier is FEP-lowered in the protonated
> state again:
>
> Article (Wang2006) Wang, J.; Deng, Y. & Roux, B. Absolute binding free
> energy calculations using molecular dynamics simulations with
> restraining potentials. Biophys J, Institute of Molecular Pediatric
> Sciences, Gordon Center for Integrative Science, University of Chicago,
> Chicago, Illinois, USA., 2006, 91, 2798-2814
>

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