- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Jason Swails <jason.swails.gmail.com>

Date: Tue, 4 Jan 2011 12:02:57 -0700

Hello,

My comments are below.

On Tue, Jan 4, 2011 at 11:03 AM, George Tzotzos <gtzotzos.me.com> wrote:

*> 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
*

*>
*

This is almost correct, but don't forget about the double-counting effect.

Residue 1 interacts with residue 2, so the non-bonded interaction between

the two residues will appear in both Residue 1 and Residue 2's decomposition

results, yet it will only be added once in the total energy. MMPBSA.py does

not calculate the total energy from selected sums of the decomposed

contributions, but rather takes the full values from the mdout file when it

parses it.

Hope this helps,

Jason

*> 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
*

*>
*

*>
*

Date: Tue, 4 Jan 2011 12:02:57 -0700

Hello,

My comments are below.

On Tue, Jan 4, 2011 at 11:03 AM, George Tzotzos <gtzotzos.me.com> wrote:

This is almost correct, but don't forget about the double-counting effect.

Residue 1 interacts with residue 2, so the non-bonded interaction between

the two residues will appear in both Residue 1 and Residue 2's decomposition

results, yet it will only be added once in the total energy. MMPBSA.py does

not calculate the total energy from selected sums of the decomposed

contributions, but rather takes the full values from the mdout file when it

parses it.

Hope this helps,

Jason

-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jan 04 2011 - 11:30:04 PST

Custom Search