Hi,
many thanks for the suggestion. I will check again the charges of my
system as well as the protonation states. In fact the "receptor"
includes as cofactor NADPH, which has a net charge of -4, mostly
delocalized on the phosphote oxygens.
Again, thanks for the hint
Matthias
Dwight McGee ha scritto:
> 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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>>
>>
>>
>
>
>
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Received on Wed May 05 2010 - 17:00:03 PDT
