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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Received on Thu Nov 17 2016 - 05:30:04 PST
