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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
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*>>
*

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*

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*

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

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:

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- application/octet-stream attachment: FINAL_DECOMP__MMPBSA.dat

- application/octet-stream attachment: FINAL_RESULTS_MMPBSA.dat

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