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
>
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>
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Received on Wed Mar 24 2010 - 20:00:02 PDT
