You have to be careful here. If you look at the statistical mechanical
equations for the entropy terms that are actually calculated in by the
normal mode analysis, these formulas make extensive use of boltzmann factors
which, in turn, are temperature dependent. Thus, you can't simply re-weight
via temperatures, you actually have to change the temperatures where they
are used in the calculation. For MMPBSA.py, there is a single "temp"
variable at the top of MMPBSA.py where all variables are defined that you
can change (this will change the T by which entropy terms are multiplied).
However, you'll also have to change the temperature in the nab code where
normal modes are calculated (in the sff/ folder, grep is your friend here)
and recompile nab, then the nmode program.
Hope this helps,
Jason
On Tue, Sep 21, 2010 at 12:41 AM, Khaled Barakat <kbarakat.ualberta.ca>wrote:
> Thank you so much. I think I can do that. This was very helpful:)
>
> Khaled
>
> On 20-Sep-10, at 10:37 PM, manoj singh wrote:
>
> > I ment to say entropic contribution to the free energy can be
> > calculated by
> > multiplication of tmp/298. Whatever entropy calculated would be the
> > entropy
> > at the simulation temp.
> >
> > On Tue, Sep 21, 2010 at 12:32 AM, manoj singh <mks.amber.gmail.com>
> > wrote:
> >
> >> As it has been said already, doing this is not advisable. However,
> >> for the
> >> entropy of solute, calculated the entropy at 298K (see the
> >> documentation)
> >> and than you can calculated the entropies at multiple temp just by
> >> multiplying it by tmp/298.
> >>
> >> Calculating the effect of change in solvent entropy is very tricky.
> >> As you
> >> are making so many simplifications already, I would say, assume
> >> this term is
> >> not contributing significantly to the change in binding affinity.
> >>
> >>
> >> On Mon, Sep 20, 2010 at 11:19 PM, Khaled Barakat <kbarakat.ualberta.ca
> >> >wrote:
> >>
> >>> I agree that multiple trajectory methods such as REMD will help in
> >>> exploring the conformational changes and extract representative
> >>> ensembles at different temperatures. However, with a large system
> >>> like
> >>> the one I am currently working on, where solvent molecules play an
> >>> important rule in bridging the interactions between the protein and
> >>> DNA, I think this my require a tremendous computational power.
> >>>
> >>> In the meantime, the entropy dependance on temperature returns me to
> >>> the first square. That is, how to specify temperature in the mm-pbsa
> >>> input file?
> >>>
> >>> Thanks for your help and the through explanation.
> >>> Khaled
> >>>
> >>> On 20-Sep-10, at 8:22 PM, manoj singh wrote:
> >>>
> >>>> Yes, I missed the two terms, the solute entropy and solvent
> >>>> entropy.
> >>>> It is
> >>>> certainly not a good practice to estimate the entropies at a diff
> >>>> temps with
> >>>> a traj created at some other temp. Provided simulation has been run
> >>>> "long
> >>>> enough", it should capture all relevant conformations with
> >>>> significant
> >>>> population at that temp, however, as mentioned, REMD can make life
> >>>> much
> >>>> easier.
> >>>>
> >>>> On Mon, Sep 20, 2010 at 10:04 PM, Thomas Cheatham <tec3.utah.edu>
> >>>> wrote:
> >>>>
> >>>>>
> >>>>>> I'm trying to run mm-pbsa at different temperatures to analyze
> >>>>>> the
> >>>>>> effects of temperature on the binding of a protein-DNA complex. I
> >>>>>> was
> >>>>>> wondering if there is a way to specify the running temperature
> >>>>>> as a
> >>>>>> parameter for the mm-pbsa script. I tried to set the temp
> >>>>>> variable
> >>>>>> to
> >>>>>> the desired temperature, but it seems there is no effect. I am
> >>>>>> using
> >>>>>> the mm-pbsa perl scripts with amber 10.
> >>>>>
> >>>>> No effect, seems correct to me. I would not expect much of an
> >>>>> effect in
> >>>>> mm-pbsa. Remember,
> >>>>>
> >>>>> deltaG = deltaH - T deltaS
> >>>>>
> >>>>> There is no temperature dependence to the "H" (loosely equivalent
> >>>>> to the
> >>>>> potential energy in the MD). Where temperature has an effect is
> >>>>> in
> >>>>> the
> >>>>> entropy term which is solute entropy (via nmode or other estimates
> >>>>> which
> >>>>> may not even be turned on in your mm-pbsa analysis since it tends
> >>>>> to be
> >>>>> expensive) and potentially the solvation free energy term although
> >>>>> this is
> >>>>> likely small in a continuum approximation...
> >>>>>
> >>>>> It is highly unlikely you will be able to get temperature
> >>>>> dependence from
> >>>>> a single trajectory at 300K since at higher temperatures a larger
> >>>>> ensemble
> >>>>> of conformations would be sampled (meaning higher entropy and
> >>>>> sampling of
> >>>>> higher potential energy structures). To get the temperature
> >>>>> dependence,
> >>>>> likely a replica-exchange approach (at minimum) would be
> >>>>> required...
> >>>>>
> >>>>> --tec3
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 21 2010 - 08:30:04 PDT
