If a carbon atom from the cofactor is far away from where it should be, this
would certainly explain the strange numbers that you are getting with the
internal energies. Are you seeing this distortion for all of the snapshots
generated by mm_pbsa.pl, or is it just one snapshot? Does it's location in
space correspond to a different atom in the complex coordinate files, or is
the atom far away from the rest of the system? You might want to double
check the numbers that you provided in the input file in the MAKECRD
section.
Good luck!
-Bill
On Thu, May 6, 2010 at 4:11 PM, Matthias Negri
<m.negri.mx.uni-saarland.de>wrote:
> Hi Ray,
> no I am following a single trajectory approach.. this is why my results
> sounds so confusing to me.
>
> However, I calculated the surface area for some snapshots and the average
> value is about 950 A^2, thus a congruent value.
>
> Interestingly, when I visualize prmtop and coordinate of the "receptor"
> (protein and cofactor) with VMD the structure looks fine, no distorted
> bonds, correct lengths, etc. Otherwise, when I visualize prmtop and
> coordinate with Sirius, a carbon atom of the cofactor seems to be far away.
> This does not happen for the complex.
>
> What can the reason be for it? Might this be related with the strange
> values emerged from the MM-PBSA calculation?
>
> Best regards,
>
> Matthias
>
>
> Ray Luo, Ph.D. ha scritto:
>
>> Matthias,
>>
>> Here are my observations of your numbers and related thoughts:
>>
>> 1) It seems that you are using the multiple trajectory approach, i.e. one
>> separate trajectory for each of complex, receptor, and ligand? Otherwise,
>> I
>> don't understand the large INT energy in the Delta G part ...
>>
>> 2) The ELE energy, i.e. gas-phase Coulombic energy, and the PBELE energy
>> are
>> both small and almost cancel out each other. This is an indication that
>> the
>> electrostatic component seems to behave reasonably well in the
>> calculation.
>>
>> 3) The PBSUR energy of -5 kcal/mol indicats a surface burial of 1000 A^2
>> upon binding if you are using a surface tension of 5 cal/mol-A^2. This
>> seems
>> to be consistent with the very negative VDW energy upon binding. Can you
>> rationalize the number for the surface burial upon binding, i.e. by doing
>> a
>> VMD visualization or some independent surface area calculation for a
>> single
>> snapshot to see whether the order of magnitude is correct?
>>
>> Good luck!
>> Ray
>>
>> On Wed, May 5, 2010 at 4:45 PM, Matthias Negri
>> <m.negri.mx.uni-saarland.de>wrote:
>>
>>
>>
>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu May 06 2010 - 14:00:03 PDT
