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
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> 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 - 22:00:07 PDT
