the answers seem to address different things - Adrian mentions needing to
have trajectory data at the temperature you want. Jason is talking about
the actual MM-PBSA program and how it needs to be changed if you want
entropies at a different T.
I think both of these are things you should consider.
On Thu, Nov 17, 2016 at 1:46 AM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Carlos,
>
> I checked archive. Jason Swail answer is as follows:
>
> Not easily. You need to modify source codes to change the temperature. The
> vibrational and rotational entropies are computed via statistical
> mechanical formulae that assume a particular temperature (and for
> quasi-harmonic entropies, you really need to use the temperature that the
> simulation was run at). And last time I checked, this temperature was
> hard-coded directly into the program, so you would need to change the
> original source code and recompile, as well as
> modify the temperature variable in MMPBSA.py, in order to try a different
> temperature.
>
> But I found same question from another person (Shahab Shariati): MM-PBSA
> calculation in different temprature:
>
> Adrian Roitberg answer is as follows:
>
> Technically yes, you have to RERUN the MD at the new temperature and rerun
> mmpbsa. You should not reuse the MD at 298 and simply change the
> temperature in mmbpsa. However, it is extremely unlikely that you will see
> statistically meaningful differences between 298 and 310 with mmbpsa.
>
> I encontered with 2 different answers. Finally, is it possible to do
> MM-GBSA in temperature other than 298.15 K?
>
> Best,
> Atila
>
> On Wed, Nov 16, 2016 at 2:42 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Always check the archives before sending email. This has been discussed
> > extensively before, and you can read the answers by typing "Mm-gbsa
> > temperature" in the search box on the amber web site.
> >
> > On Nov 16, 2016 12:42 AM, "Atila Petrosian" <atila.petrosian.gmail.com>
> > wrote:
> >
> > > Dear Amber users.
> > >
> > > I did MD simulation of my system (protein-ligand complex) in 330 K.
> > >
> > > I used obtained trajectory for MM-GBSA calculation. But in output file
> > > (*.dat), there is
> > >
> > > |All units are reported in kcal/mole.
> > > |All entropy results have units kcal/mol (Temperature is 298.15 K).
> > >
> > > I want to have Binding free energy in 330 K and not 298.15 K.
> > >
> > > How to resolve that.
> > >
> > > Best,
> > > Atila
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Received on Thu Nov 17 2016 - 05:00:02 PST
