I don't understand - you say you did md at 330K but have trajectory at
300K.
The standard program will handle 300K. If you want to estimate data at
other T, follow Jason's response.
On Nov 17, 2016 8:12 AM, "Atila Petrosian" <atila.petrosian.gmail.com>
wrote:
> Dear Carlos,
>
> Thanks for your answer.
>
> I did MD simulation of my system (protein-ligand complex) in 330 K. Thus, I
> have the trajectory data at the temperature (300 K) I want. Now, I want to
> do Binding free energy and have entropy in 300 K. How to do that?
>
> Any help will highly appreciated to help me to consider both of issues.
>
> Best,
> Atila
>
> On Thu, Nov 17, 2016 at 4:05 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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 - 05:30:03 PST
