Re: [AMBER] MMPBSA.py.MPI - Output discrepancies

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 04 Jan 2011 19:03:56 +0100

Hi Mish,

My original assumption was that DELTA G binding is the sum over all residues. For easy reference DELTA G is given in the attached FINAL_RESULTS_MMPBSA.dat and the per residue decomposition in output2.dat

I tried to add the total per-residue energies in FINAL_RESULTS_MMPBSA.dat but this does not produce the result given in FINAL_RESULTS_MMPBSA.dat. Far from it.

Most likely, I miss the whole concept.

Thanks

George





On Jan 4, 2011, at 6:22 PM, mish wrote:

> Hi George,
> When you do the per residue decomposition of the enthalpic part of free
> energy, the script calculates teh contribution of each specified residue.
> Are u decomposing it over all the residues and reporting sum of all the
> residues over here like-
> DELTA G binding = -46.6213 +/- 3.1112 0.1663
> (given by per-residue entropy decomposition)
>
> so is it the sum over all the residues ??
>
> ..mish
>
> On Tue, Jan 4, 2011 at 12:02 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>>
>>>> _______________________________________________
>>>> 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



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Jan 04 2011 - 10:30:02 PST
Custom Search