On Wed, Jan 14, 2015 at 6:24 AM, Federica Chiappori <
federica.chiappori.itb.cnr.it> wrote:
> Dear Amber,
> I will perform a Free Energy Perturbation to evaluate the effect of a
> mutation. If I correctly understand the Amber module to perform FEP is the
> Gibbs module, but the last version including this module is the Amber7.
>
If you can implement a mutation by creating prmtop files that interpolate
between two "end-state" prmtops, then you can run FEP calculations by
simulating each window directly in sander/pmemd and post-processing the
resulting trajectories to extract the FEP free energy (either using the
basic FEP equations or something a bit more sophisticated like MBAR).
ParmEd makes it easy to scale charges, and with a little work can
interpolate van der Waals parameters as well.
You can also use the H-REMD functionality in sander/pmemd to implement
replica exchange free energy perturbation (REFEP). For example the
following H-REMD/REFEP study was carried out using this functionality
currently implemented in Amber:
http://pubs.acs.org/doi/abs/10.1021/ct200153u
It is possible to obtain this module separately?
>
As far as I understand, it would not be feasible to run GIBBS for a
current study now, even if someone was able to dig up the source code.
>
> I have Amber 12 and Amber14 available, is there any other tool to perform
>
> FEP?
>
Outside of what I described above, no other part of Amber (that I'm
familiar with) supports FEP.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 14 2015 - 16:30:02 PST
