Hi,
In my experiences I have only seen cases where the DELTA G was very high
when certain things such as the ligand or residues from the receptor which
interact w/ the ligand were not protonated correctly. As a suggestion I
would make absolutely certain that everything has the correct charge. Good
luck
On Wed, May 5, 2010 at 6:17 AM, Matthias Negri
<m.negri.mx.uni-saarland.de>wrote:
> Hello to everyone,
> I'm experiencing some problems in an MM-PBSA calculation. My system
> consists of enzyme, cofactor (NADPH) and inhibitor. Previous calculations
> (on different enzyme conformers) run fine, while for this specific case the
> final delta PBTOT I obtained is way to large (-324.94), mostly due to an
> imbalanced delta GAS (-356.32; in particular my delta INT is -120.87 and
> delta VdW is -216.83). The topology files and the crd of complex, receptor
> and ligand look nice when I visualize them in VMD), no bonds are distorted
> or broken, etc.
>
> Hereafter my output file of the MM-PBSA calculation:
>
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -7236.85 96.82 -7192.48 96.10 -25.76
> 0.48
> VDW -1199.12 28.96 -993.70 30.53 11.41
> 1.22
> INT 5792.37 46.59 5882.25 51.16 30.99
> 3.65
> GAS -2643.60 103.44 -2303.93 106.04 16.64
> 3.53
> PBSUR 104.29 1.24 105.77 1.26 3.44
> 0.02
> PBCAL -3415.05 88.12 -3424.16 88.17 -27.19
> 0.51
> PBSOL -3310.76 87.43 -3318.39 87.45 -23.75
> 0.51
> PBELE -10651.91 32.14 -10616.63 32.91 -52.95
> 0.58
> PBTOT -5954.37 44.68 -5622.32 51.50 -7.11
> 3.48
>
> # DELTA # -----------------------
> # MEAN STD
> # =======================
> ELE -18.62 6.32
> VDW -216.83 5.70
> INT -120.87 16.97
> GAS -356.32 17.62
> PBSUR -4.92 0.17
> PBCAL 36.30 4.20
> PBSOL 31.38 4.23
> PBELE 17.68 5.12
> PBTOT -324.94 17.04
>
> What can the reason for such huge energy differences be? Where should I
> search for the mistake (If any is in)?
>
> Attached you can find input, output for the mm-pbsa calculation, as well as
> prmtop and crd of ligand, "receptor (protein and cofactor)" and complex.
>
> Many thanks,
>
> Matthias Negri
>
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>
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed May 05 2010 - 08:30:06 PDT
