On Sun, Nov 20, 2016 at 3:52 AM, Atila Petrosian
<atila.petrosian.gmail.com> wrote:
>> 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).
To clarify; the temperature restriction was removed from the code in
cpptraj that MMPBSA.py uses on the back-end for the quasi-harmonic
calculation. In order to use it you will need to modify MMPBSA.py as
Jason suggested.
-Dan
>
>
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sun Nov 20 2016 - 04:30:03 PST
