I really had a doubt on ligand snapshots because average vdw you shown for
ligand are quite high (195120.40) compared to protein and complex. Which is
kind of strange for me. If you are getting correct values from python
scripts (for same snapshots) then it is likely not to an issue related to
GAFF you got for ligand. Nevertheless, structure you sent to me looks quite
OK. Please be sure that you are using correct structures during the
calculation and if you are sure about it then can I also have a look in
complex's and protein's snapshot and their top file ?
On Wed, Feb 1, 2012 at 9:02 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
>
> Dear Mish,
>
> I attached the prmtop and snapshot file,
>
> Urszula
> ________________________________________
> Von: Sushil Mishra [sushilbioinfo.gmail.com]
> Gesendet: Mittwoch, 1. Februar 2012 08:53
> An: AMBER Mailing List
> Betreff: Re: [AMBER] MMPBSA problem
>
> Can you please forward one snapshot of ligand and LIG.prmtop file only ?
>
> ..Mish
>
> On Wed, Feb 1, 2012 at 8:36 AM, Urszula Uciechowska
> <urszula.uciechowska.chem.umu.se> wrote:
> > Yes I have checked that, and they looked correct ...
> >
> > /Urszula
> > ________________________________________
> > Von: mish [smncbr.gmail.com]
> > Gesendet: Mittwoch, 1. Februar 2012 07:41
> > An: AMBER Mailing List
> > Betreff: Re: [AMBER] MMPBSA problem
> >
> > Hello,
> >
> > It sound like that there are some vdW clashes in the snapshots. Do you
> see
> > the correct structure of complex, protein and ligand when you load their
> > snapshots with COM.prmtop, REC,prmtop and LIG.prmtop * from same
> directory)
> > in vmd ?. If you have not tried it, just check the structures properly so
> > that one can be sure that snapshots generated here are correct for
> > the particular topology file.
> >
> > ..Mish
> >
> > On Wed, Feb 1, 2012 at 7:26 AM, Urszula Uciechowska <
> > urszula.uciechowska.chem.umu.se> wrote:
> >
> >> Dear Amber users,
> >>
> >> I am running MMPBSA calcuations for 100sps, my input file for that is:
> >>
> >> #
> >> # Input parameters for mm_pbsa.pl
> >> #
> >> #
> >>
> >>
> ################################################################################
> >> #
> >> VERBOSE 0
> >> PARALLEL 0
> >> #
> >> PREFIX L
> >> PATH ./
> >> START 1
> >> STOP 1
> >> OFFSET 1
> >> #
> >> COMPLEX 1
> >> RECEPTOR 1
> >> LIGAND 1
> >> #
> >> COMPT ./COM.prmtop
> >> RECPT ./REC.prmtop
> >> LIGPT ./LIG.prmtop
> >> #
> >> GC 0
> >> AS 0
> >> DC 0
> >> #
> >> MM 1
> >> GB 1
> >> PB 1
> >> MS 1
> >> #
> >> NM 0
> >> #
> >>
> >>
> ################################################################################
> >> #
> >> PROC 2
> >> REFE 0
> >> INDI 1.0
> >> EXDI 80.0
> >> SCALE 2
> >> LINIT 1000
> >> PRBRAD 1.4
> >> ISTRNG 0.0
> >> RADIOPT 0
> >> INP 1
> >> #
> >> SURFTEN 0.04356
> >> SURFOFF -1.008
> >> #
> >> IVCAP 0
> >> CUTCAP -1.0
> >> XCAP 0.0
> >> YCAP 0.0
> >> ZCAP 0.0
> >> #
> >>
> >>
> ################################################################################
> >> .MM
> >> #
> >> # MM parameters (this section is only relevant if MM = 1 above)
> >> #
> >> # The following parameters are passed to sander.
> >> # For further details see the sander documentation.
> >> #
> >> # DIELC - Dielectricity constant for electrostatic interactions.
> >> # Note: This is not related to GB calculations.
> >> #
> >> DIELC 1.0
> >> #
> >>
> >>
> ################################################################################
> >> # the desolvation according to Gnp = SURFTEN * SASA +
> >> SURFOFF.
> >> #
> >> IGB 5
> >> GBSA 1
> >> SALTCON 0.00
> >> EXTDIEL 80.0
> >> INTDIEL 1.0
> >> #
> >> SURFTEN 0.0072
> >> SURFOFF 0.00
> >> #
> >>
> >>
> ################################################################################
> >> .MS
> >> #
> >> # Molsurf parameters (this section is only relevant if MS = 1 above)
> >> #
> >> # PROBE - Radius of the probe sphere used to calculate the SAS.
> >> # In general, since Bondi radii are already augmented by 1.4A,
> >> # PROBE should be 0.0
> >> # In IVCAP = 1 or 5, the solvent excluded surface is required
> for
> >> # calculating the cavity contribution. Bondi radii are not
> >> # augmented in this case and PROBE should be 1.4.
> >> #
> >> PROBE 0.0
> >> #
> >>
> >>
> ################################################################################
> >>
> >> but the energy that I am getting is huge ...
> >>
> >>
> >>
> >>
> >> # COMPLEX RECEPTOR
> LIGAND
> >> # ----------------------- -----------------------
> >> -----------------------
> >> # MEAN STD MEAN STD MEAN
> >> STD
> >> # ======================= =======================
> >> =======================
> >> ELE -10841.03 101.25 -10410.47 96.18 -190.08
> >> 17.55
> >> VDW -1543.33 28.21 -1466.58 27.14 195120.40
> >> 4894.33
> >> INT 8334.19 51.25 8119.96 49.62 168750.44
> >> 12093.84
> >> GAS -4050.18 109.39 -3757.09 105.02 363680.75
> >> 13158.43
> >> PBSUR 927.79 6.78 927.94 6.33 77.73
> >> 1.32
> >> PBCAL -6405.31 89.46 -6405.69 83.25 -437.07
> >> 13.88
> >> PBSOL -5477.52 87.33 -5477.76 80.88 -359.33
> >> 14.13
> >> PBELE -17246.34 36.97 -16816.16 36.62 -627.15
> >> 9.25
> >> PBTOT -9527.70 53.87 -9234.85 52.03 363321.42
> >> 13157.67
> >> GBSUR 153.52 1.12 153.54 1.05 13.02
> >> 0.22
> >> GB -3611.13 96.16 -3775.40 90.77 -310.76
> >> 13.24
> >> GBSOL -3457.61 95.80 -3621.85 90.41 -297.75
> >> 13.26
> >> GBELE -14452.16 62.85 -14185.86 58.91 -500.85
> >> 11.48
> >> GBTOT -7507.79 78.59 -7378.94 75.06 363383.00
> >> 13157.15
> >>
> >> # DELTA
> >> # -----------------------
> >> # MEAN STD
> >> # =======================
> >> ELE -240.48 140.75
> >> VDW -195197.15 4894.48
> >> INT -168536.20 12094.05
> >> GAS -363973.84 13159.30
> >> PBSUR -77.88 9.37
> >> PBCAL 437.45 122.98
> >> PBSOL 359.57 119.87
> >> PBELE 196.97 52.85
> >> PBTOT -363614.26 13157.88
> >> GBSUR -13.04 1.55
> >> GB 475.03 132.90
> >> GBSOL 461.99 132.39
> >> GBELE 234.55 86.90
> >> GBTOT -363511.84 13157.60
> >>
> >>
> >> when I am running MMPBSA.py for the same snapshots the energies are :
> >> Differences (Complex - Receptor - Ligand):
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -86.1604 4.7220
> >> 0.4722
> >> EEL -322.6536 22.3014
> >> 2.2301
> >> EGB 357.6727 20.9844
> >> 2.0984
> >> ESURF -12.0810 0.4190
> >> 0.0419
> >>
> >> DELTA G gas -408.8140 20.9551
> >> 2.0955
> >> DELTA G solv 345.5916 20.9989
> >> 2.0999
> >>
> >>
> >> DELTA G binding = -63.2223 +/- 3.8132
> >> 0.3813
> >>
> >>
> >> What is the problem here? For MMPBSA.py I am not able to get PB energy,
> >> with GB there is no problem...
> >> Thank you in advance for any suggestions,
> >>
> >> /Urszula
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 01 2012 - 01:00:03 PST
