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
>>
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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 - 23:00:03 PDT
