then you need to read Jason's email and follow his advice.
On Thu, Nov 17, 2016 at 8:22 AM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Excuse me. Considered temperature is 330 K in my project.
>
> On Thu, Nov 17, 2016 at 4:42 PM, 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
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 17 2016 - 06:00:04 PST
