Apologies,
I meant per residue free energy decomposition (see
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm)
Thanks
George
On Jan 4, 2011, at 11:52 AM, mish wrote:
> On Tue, Jan 4, 2011 at 11:41 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Happy New Year to all,
>>
>> I've been running MMPBSA.py.MPI to determine Delta G for a protein-ligand.
>> I've also run the program to determine per residue decomposition of entropy.
>>
>> The same input files have been used in both cases. The the Delta G results
>> obtained from Generalized Born differ by ~ 2kcal/mol
>>
>> For example,
>>
>> Differences (Complex - Receptor - Ligand):
>>
>> DELTA G binding = -46.6213 +/- 3.1112
>> 0.1663 (given by per-residue entropy
>> decomposition)
>>
> what do u mean by per residue entropy decomposition ?
>
>> DELTA G binding = -44.2279 +/- 2.7619
>> 0.1476 (without per-residue entropy
>> decomposition)
>>
>> The same discrepancy of ~2kcal/mol has been observed using the same ligand
>> with two (2) other receptors.
>>
>> The Poisson Boltzmann calculations with and without per residue
>> decomposition gave identical values
>>
>> Differences (Complex - Receptor - Ligand):
>>
>> DELTA G binding = -34.0898 +/- 3.1112
>> 0.1663
>>
>> My specific questions are the following:
>>
>> 1. Is there an explanation for this discrepancy in the case of Generalized
>> Born while this discrepancy is not observed in the Poisson Boltzmann
>> calculations?
>>
>> 2. The Delta Gs given by the two methods are different by ~10 kcal/mol.
>> That strikes me as being too much of a difference.
>>
>> 3. Is temperature (say 300K) factored in the ENTROPY calculations?
>>
>> 4. Can one assume that the enthalpy for the six translational and
>> rotational degrees of freedom is 6*(1/2)*RT=1.8 kcal/mol at 300K?
>> (are u talking about expected entropy or enthalpy ? )
>> Thanks in advance and best regards
>>
>> George
>>
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Received on Tue Jan 04 2011 - 03:30:02 PST
