Dear Ray
Thanks a lot, you reply was very helpful
Regards
Emilio
> Date: Sat, 5 Jan 2013 16:57:09 -0800
> From: ray.luo.uci.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA
>
> Emilio,
>
> A possible reason is that the net charges of the protein and of the
> ligand have the same sign even if there is a salt bridge at the
> binding site.
>
> The changes in the electrostatic solvation energy and the Coulomb
> energy upon binding in general have the opposite signs. This can be
> understood by looking at the GB formula: there is a pairwise
> (interaction) term that scales as q_i x q_j. This is similar to the
> pairwise term in the Coulomb energy. This term would have the same
> sign as the pairwise Coulomb term if it were without the pre-factor of
> (1 - 1/80) since the pre-factor is always negative.
>
> Hope this helps.
>
> Ray
>
> On Sat, Jan 5, 2013 at 11:44 AM, Emilio Angelina
> <emilioluisangelina.hotmail.com> wrote:
> >
> > Dear all,
> > I have performed MD simulations and MMPBSA analysis on a series of ligands in the binding site of a GPCR receptor. It seems strange to me that DeltaEEL be positive since in my case there is a salt bridge between the receptor and the ligand. It also seems strange for the same reasons that DeltaEGB be negative.
> > The FINAL_RESULTS_MMPBSA.dat output is shown below.
> > GENERALIZED BORN:
> > WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIALTERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLEComplex:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------BOND 1283.9138 32.9110 3.2748ANGLE 3568.7667 51.8214 5.1564DIHED 4557.0217 26.1060 2.5976VDWAALS -3119.2732 21.5280 2.1421EEL -21488.9966 190.9942 19.00461-4 VDW 1573.5725 17.9417 1.78531-4 EEL 14660.8743 52.6229 5.2362EGB -9743.1158 179.9175 17.9025ESURF 180.1894 2.0514 0.2041
> > G gas 1035.8792 194.0832 19.3120G solv -9562.9264 178.4552 17.7570
> > TOTAL -8527.0472 63.3810 6.3066
> >
> > Receptor:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------BOND 1275.5349 32.8067 3.2644ANGLE 3552.1022 51.5383 5.1283DIHED 4548.2534 25.9616 2.5833VDWAALS -3080.9085 20.9271 2.0823EEL -21560.8980 199.0677 19.80801-4 VDW 1559.6602 17.9804 1.78911-4 EEL 14689.5611 52.5279 5.2267EGB -9648.9484 185.7658 18.4844ESURF 181.6462 2.0381 0.2028
> > G gas 983.3052 201.4158 20.0416G solv -9467.3022 184.3024 18.3388
> > TOTAL -8483.9969 63.9539 6.3637
> >
> > Ligand:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------BOND 8.3789 2.3596 0.2348ANGLE 16.6645 2.7870 0.2773DIHED 8.7705 2.0843 0.2074VDWAALS -3.7118 0.2799 0.0278EEL 34.3090 1.9865 0.19771-4 VDW 13.9123 1.2700 0.12641-4 EEL -28.6868 1.6891 0.1681EGB -61.4325 0.9973 0.0992ESURF 3.5740 0.0242 0.0024
> > G gas 49.6366 5.1081 0.5083G solv -57.8585 0.9923 0.0987
> > TOTAL -8.2219 4.5763 0.4554
> >
> > Differences (Complex - Receptor - Ligand):Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------BOND 0.0000 0.0001 0.0000ANGLE 0.0000 0.0001 0.0000DIHED -0.0022 0.0065 0.0006VDWAALS -34.6528 2.7104 0.2697EEL 37.5924 15.8707 1.57921-4 VDW -0.0000 0.0001 0.00001-4 EEL 0.0000 0.0001 0.0000EGB -32.7349 10.7173 1.0664ESURF -5.0308 0.0796 0.0079
> > DELTA G gas 2.9374 15.3958 1.5319DELTA G solv -37.7657 10.7322 1.0679
> > DELTA TOTAL -34.8283 5.5203 0.5493
> > Please suggest the source of error in this calculation. Thank you in advance
> > Emilio Angelina Universidad Nacional del Nordeste Corrientes, Argentina
> >
> >
> >
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Received on Sat Jan 05 2013 - 20:30:03 PST
