extract_coords.mmpbsa and binding_energy.mmpbsa are the ones mentioned in
the tutorial
On Fri, Mar 26, 2010 at 2:18 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com>wrote:
> 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 - 02:00:04 PDT
