Dear Dan,
Thanks for your answer.
> What version of AmberTools are you using?
I'm using AmberTools 14.
> I'm pretty certain the 298 K temperature restriction was removed sone
time ago.
Are you sure??? There is the following sentence in MM-GBSA output file.
|All entropy results have units kcal/mol (Temperature is 298.15 K).
Dear Jason,
Thanks for your answer.
>> 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.
I ran MD simulation at the desired temperature (310 K).
>> 2. For quasi-harmonic analysis, 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).
I'm a beginner in modifying source codes. Please help me to do that step by
step.
Is not a tutorial about doing MM-GBSA at different temperatures?
Thanks,
Atila
On Thu, Nov 17, 2016 at 9:25 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> > >> > > > _______________________________________________
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>
> --
> Jason M. Swails
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Received on Sun Nov 20 2016 - 01:00:03 PST
