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
>>
> _______________________________________________
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> 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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Received on Wed Mar 24 2010 - 22:00:04 PDT
