Soumya,
Can you attach your **com.all.out , **rec.all.out and your **lig.all.out?
On Thu, Mar 25, 2010 at 1:41 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Mar 24, 2010 at 9:57 PM, Shulin Zhuang <shulin.zhuang.gmail.com>
> wrote:
> > As far as I know, "No skew or curtosis when zero variance in moment",
> this
> > would not affect the result. I once repeat the mm-pbsa tutorial and got
> the
> > same result with this message.
> > shulin
>
> This is true, since this is simply stating that there is no third or
> fourth moments in the dataset. However, the values obtained for the
> free energy of binding I can't rationalize. -14,000 kcal/mol binding
> free energy for any solvent model seems ridiculously high for a
> complex-receptor-ligand system. I would still visualize some of the
> receptor, ligand, and complex snapshots with their respective prmtop
> files to see if a problem jumps out at you.
>
> Good luck!
> Jason
>
> >
> > On Wed, Mar 24, 2010 at 9:47 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> Hello,
> >>
> >> These values still appear too large. When you stripped the water
> >> molecules from the coordinate files, did you also remove the box
> >> information?
> >>
> >> Good luck!
> >> Jason
> >>
> >> On Wed, Mar 24, 2010 at 7:52 PM, Soumya Lipsa Rath
> >> <soumyalipsabt.gmail.com> wrote:
> >> > I rechecked my inputs, the error was in the input crd files where I
> had
> >> > stripped the water,I still get "No skew or curtosis when zero variance
> in
> >> > moment" and my output now shows the following, is it fine now?
> >> >
> >> > # COMPLEX RECEPTOR
> >> > LIGAND
> >> > # ----------------------- -----------------------
> >> > -----------------------
> >> > # MEAN STD MEAN STD
> >> > MEAN STD
> >> > # ======================= =======================
> >> > =======================
> >> > ELE -20984.47 136.03 -8850.44 116.06
> -11190.81
> >> > 118.86
> >> > VDW -2358.31 46.14 -1196.51 30.18
> -1510.23
> >> > 34.65
> >> > INT 15920.80 90.00 7354.56 58.60
> 8566.24
> >> > 60.88
> >> > GAS -7421.98 167.97 -2692.39 141.05
> -4134.80
> >> > 130.31
> >> > PBSUR 230.36 2.51 114.95 1.71
> >> > 149.35 1.99
> >> > PBCAL -7595.54 135.74 -3530.88 105.61
> -5107.11
> >> > 105.58
> >> > PBSOL -7365.18 134.59 -3415.93 104.36
> -4957.76
> >> > 104.70
> >> > PBELE -28580.01 61.99 -12381.33 29.99
> -16297.92
> >> > 52.71
> >> > PBTOT -14787.16 73.06 -6108.32 57.35
> -9092.56
> >> > 67.74
> >> > GBSUR 230.36 2.51 114.95 1.71
> >> > 149.35 1.99
> >> > GB -7734.58 137.55 -3563.37 112.09
> -5222.03
> >> > 109.39
> >> > GBSOL -7504.22 136.54 -3448.41 110.86
> -5072.68
> >> > 108.62
> >> > GBELE -28719.05 55.47 -12413.81 30.01
> -16412.84
> >> > 38.12
> >> > GBTOT -14926.20 67.49 -6140.80 53.70
> -9207.48
> >> > 59.61
> >> >
> >> > # DELTA
> >> > # -----------------------
> >> > # MEAN STD
> >> > # =======================
> >> > ELE -943.22 53.10
> >> > VDW 348.43 19.64
> >> > INT -0.00 0.00
> >> > GAS -594.79 56.70
> >> > PBSUR -33.94 1.23
> >> > PBCAL 1042.45 51.98
> >> > PBSOL 1008.51 51.56
> >> > PBELE 99.23 13.12
> >> > PBTOT 413.72 22.10
> >> > GBSUR -33.94 1.23
> >> > GB 1050.82 49.69
> >> > GBSOL 1016.87 49.26
> >> > GBELE 107.60 9.26
> >> > GBTOT 422.08 20.09
> >> >
> >> >
> >> >
> >> > On Wed, Mar 24, 2010 at 11:51 AM, Jason Swails <
> jason.swails.gmail.com
> >> >wrote:
> >> >
> >> >> Hello,
> >> >>
> >> >> It appears as though your van der waals and internal coordinate
> >> >> (bond,angle,dihedral) parameters are going crazy. This is typically
> >> >> caused by overlapping atoms or incompatible prmtops (i.e. prmtop
> files
> >> >> that do not correspond to the coordinates from the trajectories). I
> >> >> would try to visualize your snapshots using some kind of
> visualization
> >> >> program like pymol or vmd. I'm guessing this would reveal right away
> >> >> some problems.
> >> >>
> >> >> Good luck!
> >> >> Jason
> >> >>
> >> >> On Tue, Mar 23, 2010 at 9:51 PM, Soumya Lipsa Rath
> >> >> <soumyalipsabt.gmail.com> wrote:
> >> >> > Hello,
> >> >> >
> >> >> > This is my input file :
> >> >> > .GENERAL
> >> >> > PREFIX snapshot
> >> >> > PATH ./
> >> >> > 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
> >> >> > .PB
> >> >> > PROC 2
> >> >> > REFE 0
> >> >> > INDI 1.0
> >> >> > EXDI 80.0
> >> >> > SCALE 2
> >> >> > LINIT 1000
> >> >> > PRBRAD 1.4
> >> >> > ISTRNG 0.0
> >> >> > RADIOPT 0
> >> >> > NPOPT 1
> >> >> > CAVITY_SURFTEN 0.0072
> >> >> > CAVITY_OFFSET 0.00
> >> >> > SURFTEN 0.0072
> >> >> > SURFOFF 0.00
> >> >> > .MM
> >> >> > DIELC 1.0
> >> >> > .GB
> >> >> > IGB 2
> >> >> > GBSA 1
> >> >> > SALTCON 0.00
> >> >> > EXTDIEL 80.0
> >> >> > INTDIEL 1.0
> >> >> > SURFTEN 0.0072
> >> >> > SURFOFF 0.00
> >> >> > .MS
> >> >> > PROBE 0.0
> >> >> > .PROGRAMS
> >> >> >
> >> >> > My output file statistics.out:# COMPLEX
> >> >> > RECEPTOR LIGAND
> >> >> > # ----------------------- -----------------------
> >> >> > -----------------------
> >> >> > # MEAN STD MEAN STD
> >> >> > MEAN STD
> >> >> > # ======================= =======================
> >> >> > =======================
> >> >> > ELE -17639.56 1641.66 -8035.60 790.05
> >> -9620.29
> >> >> > 873.88
> >> >> > VDW 41234766.61 10845556.46 17173433.65 4686036.34
> >> 24575897.25
> >> >> > 6727343.07
> >> >> > INT 24824456.41 7331052.92 10781518.04 5200319.05
> >> 14042938.37
> >> >> > 6280267.67
> >> >> > GAS 66041583.46 17205330.73 27946916.08 8283405.63
> >> 38609215.33
> >> >> > 11272008.74
> >> >> > PBSUR 222.18 3.17 134.88 10.18
> >> >> > 164.59 6.86
> >> >> > PBCAL -14722.85 1851.76 -7071.37 1107.07
> >> -10464.38
> >> >> > 1573.20
> >> >> > PBSOL -14500.67 1854.35 -6936.49 1099.30
> >> -10299.80
> >> >> > 1568.06
> >> >> > PBELE -32362.41 1863.56 -15106.98 1071.87
> >> -20084.68
> >> >> > 1294.56
> >> >> > PBTOT 66027082.79 17203619.08 27939979.59 8282541.01
> >> 38598915.53
> >> >> > 11270705.78
> >> >> > GBSUR 222.18 3.17 134.88 10.18
> >> >> > 164.59 6.86
> >> >> > GB -17315.63 2469.17 -7872.55 1184.63
> >> -11779.30
> >> >> > 1792.69
> >> >> > GBSOL -17093.45 2471.57 -7737.67 1178.32
> >> -11614.71
> >> >> > 1788.45
> >> >> > GBELE -34955.19 2086.22 -15908.15 1075.87
> >> -21399.59
> >> >> > 1421.19
> >> >> > GBTOT 66024490.00 17202998.84 27939178.42 8282465.01
> >> 38597600.62
> >> >> > 11270432.07
> >> >> >
> >> >> > # DELTA
> >> >> > # -----------------------
> >> >> > # MEAN STD
> >> >> > # =======================
> >> >> > ELE 16.34 933.41
> >> >> > VDW -514564.29 1852217.24
> >> >> > INT -0.00 0.00
> >> >> > GAS -514547.96 1851444.75
> >> >> > PBSUR -77.29 14.60
> >> >> > PBCAL 2812.91 787.27
> >> >> > PBSOL 2735.62 775.07
> >> >> > PBELE 2829.24 1270.12
> >> >> > PBTOT -511812.34 1851493.98
> >> >> > GBSUR -77.29 14.60
> >> >> > GB 2336.21 497.67
> >> >> > GBSOL 2258.92 486.39
> >> >> > GBELE 2352.55 1100.29
> >> >> > GBTOT -512289.03 1851446.30
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Tue, Mar 23, 2010 at 8:02 PM, Dwight McGee <
> dwight.mcgee.gmail.com
> >> >> >wrote:
> >> >> >
> >> >> >> Hi Soumya,
> >> >> >>
> >> >> >>
> >> >> >> The error which posted "No skew or curtosis when zero variance in
> >> >> moment"
> >> >> >> comes from the mm_pbsa_statistics.pm. If you could attach your
> >> output
> >> >> >> files
> >> >> >> from mm_pbsa.pl and your input files I might can offer greater
> >> insight
> >> >> >> into
> >> >> >> what is exactly happening.
> >> >> >>
> >> >> >> On Tue, Mar 23, 2010 at 4:21 AM, Soumya Lipsa Rath
> >> >> >> <soumyalipsabt.gmail.com>wrote:
> >> >> >>
> >> >> >> > Hello,
> >> >> >> >
> >> >> >> > I am trying to run MMPBSA to calculate the binding energy .
> Besides
> >> >> >> getting
> >> >> >> > the frequently reported error
> >> >> >> > "No skew or curtosis when zero variance in moment" . The values
> in
> >> my
> >> >> >> > statistics.out file are high.
> >> >> >> > I also tried running the examples (in the /src/mm_pbsa/Examples
> )
> >> but
> >> >> I
> >> >> >> > still get the same error. What can be done to rectify this
> error?
> >> >> >> >
> >> >> >> > (Strangely when I decrease the NFREQ value I get additional
> errors
> >> >> like
> >> >> >> > vertex atom mismatch.)
> >> >> >> >
> >> >> >> > Regards,
> >> >> >> >
> >> >> >> > Soumya
> >> >> >> > _______________________________________________
> >> >> >> > AMBER mailing list
> >> >> >> > AMBER.ambermd.org
> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> 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
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> ---------------------------------------
> >> >> Jason M. Swails
> >> >> Quantum Theory Project,
> >> >> University of Florida
> >> >> Ph.D. Graduate Student
> >> >> 352-392-4032
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> ---------------------------------------
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Thu Mar 25 2010 - 07:30:03 PDT
