As things stand now, temperature comes into play in 3 places:
1. The trajectory must be run at the desired temperature to ensure the
proper Boltzmann distribution of snapshots at that temperature. This is all
that's necessary to get the "correct" PB or GB energies at the desired
temperature.
2. For quasi-harmonic analysis, the the temperature needs to be provided to
cpptraj. However, MMPBSA.py does not expose this variable, since ptraj did
not support specifying the temperature at the time that MMPBSA.py was
written. So you need to change the MMPBSA.py source code to modify the
input file given to cpptraj (create_input.py)
3. For normal mode calculation, nab itself is hard-coded to use 298.15 as
temperature in several places (look in nmode.c in
$AMBERHOME/AmberTools/src/sff). You will need to adjust the code with the
new temperature, then recompile AmberTools.
For both 2 and 3, you will need to modify the MMPBSA.py source code to
specify a different temperature (this only affects what the entropy results
get multiplied by). Look for line 765 of main.py.
The take-home message is that changing temperatures for entropy calculation
in MMPBSA.py is not easy, and you should carefully check that any changes
you make have the expected effect. The first piece of advice to performing
MM/PBSA analyses is to make sure you can do it "by hand" first, before
using either of the scripts. That is particularly good advice here.
HTH,
Jason
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
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 17 2016 - 10:00:05 PST
