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 Wed Nov 16 2016 - 23:00:02 PST
