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
>
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Received on Tue Mar 23 2010 - 22:00:03 PDT
