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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
Received on Mon Sep 20 2010 - 22:00:05 PDT
