Hi Federica,>I will perform TI as explained in the amber14 reference manual.
>I'm employing pmemd to perform these simulations because I'm using a GPU
>server.
I don't think that TI calculations are supported by the GPU version. Am I right?
Regards,Filip
On Wednesday, January 28, 2015 12:11 PM, Federica Chiappori <federica.chiappori.itb.cnr.it> wrote:
Dear all, thank you for your answers and suggestions.
Finally, I will perform TI as explained in the amber14 reference manual.
I'm employing pmemd to perform these simulations because I'm using a GPU
server.
In the reference manual is described how to obtain a single topology file
for wt and mutant proteins, but there is not described how does the group
file looks like (pag. 351). In particular: mdin and prmtop are the same
files for both lines and only the outputs are different, are both line
necessary? Or with the new commands (timask and scmask) I will obtain all
the informations in a single file?
Many thanks for helping me.
Federica
On 15 January 2015 at 01:10, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> 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
>
--
Federica Chiappori, Ph.D.
Istituto di Tecnologie Biomediche - CNR
Via F.lli Cervi, 93
20090 Segrate (MI)
Phone: +39 02 26422606
E-mail: federica.chiappori.itb.cnr.it
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Received on Wed Jan 28 2015 - 10:30:03 PST
