Re: [AMBER] MMPBSA error

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 24 Mar 2010 21:47:48 -0700

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
>> >> _______________________________________________
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>> >>
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>> >
>>
>>
>>
>> --
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
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>>
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-- 
---------------------------------------
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
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