Hi, Shulin, I am not stripping water these are the steps which I did:
a) Generate x.prmtop and x.inpcrd of the complex receptor and ligand
b) Add water run MD
c) run the extract_coords.mmpbsa files renaming the top files and inputting
the trajectory
d) this in turn generates the stripped crd files then I run the
binding_energy.mmpbsa
On Fri, Mar 26, 2010 at 11:52 AM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:
> Hi, Soumya, when generating the snapshot, you do not need strip water.
>
> On Thu, Mar 25, 2010 at 8:43 PM, Soumya Lipsa Rath
> <soumyalipsabt.gmail.com>wrote:
>
> > Hello,
> >
> > No Jason, I haven't removed the box information after stripping water....
> > I have attached here my **com.all.out , **rec.all.out and **lig.all.out
> > files
> >
> > Regards,
> > Soumya
> >
> > On Thu, Mar 25, 2010 at 7:38 PM, Dwight McGee <dwight.mcgee.gmail.com
> > >wrote:
> >
> > > Soumya,
> > >
> > > Can you attach your **com.all.out , **rec.all.out and your
> **lig.all.out?
> > >
> > > On Thu, Mar 25, 2010 at 1:41 AM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > 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
> > > > >>
> > > > > _______________________________________________
> > > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > 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
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 26 2010 - 02:00:03 PDT
