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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Received on Mon Sep 20 2010 - 22:00:08 PDT
