Try using MMPBSA.py. It has better error-checking, and the people
responding on this list are experts with that version, not the perl one.
It's released freely with AmberTools 1.5.
All the best,
Jason
On Sun, May 8, 2011 at 10:43 AM, mirage . <m.o.m.live.fr> wrote:
>
>
>
>
> Thanks for reply,
>
> How to prevent to obtain INT not zero if i do my MD another time
>
> 1/ When you say the delta INT value is not zero, what is it? How far away
> from zero is it?
>
>
> # COMPLEX OMPLEX RECEPTOR
> LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -49.06 9.51 -33.14 9.07 -12.82
> 2.20
> VDW -130.64 14.36 -55.78 9.38 12.98
> 2.73
> INT 1010.19 18.38 878.10 16.52 139.73
> 8.29
> GAS 830.49 24.57 789.18 18.93 139.89
> 9.62
> PBSUR 25.97 1.52 27.41 1.05 10.13
> 0.16
> PBCAL -174.92 111.66 -174.23 7.45 -13.60
> 1.77
> PBSOL -148.95 111.68 -146.82 6.98 -3.47
> 1.77
> PBELE -223.98 111.63 -207.37 6.39 -26.42
> 0.82
> PBTOT 681.54 114.33 642.36 17.09 136.42
> 8.77
> GBSUR 25.97 1.52 27.41 1.05 10.13
> 0.16
> GB -126.15 7.30 -132.27 5.81 -11.58
> 1.60
> GBSOL -100.19 6.50 -104.86 5.38 -1.45
> 1.59
> GBELE -175.21 6.03 -165.41 5.58 -24.39
> 0.94
> GBTOT 730.30 21.69 684.32 17.25 138.44
> 8.83
> TSTRA 15.34 0.00 15.20 0.00 13.62
> 0.00
> TSROT 15.00 0.18 14.90 0.21 12.78
> 0.07
> TSVIB 479.80 6.43 409.55 7.48 82.28
> 3.22
> TSTOT 510.15 6.52 439.65 7.55 108.68
> 3.21
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -3.10 2.69
> VDW -87.83 8.69
> INT -7.65 0.92
> GAS -98.58 9.75
> PBSUR -11.57 0.83
> PBCAL 12.91 111.59
> PBSOL 1.34 111.63
> PBELE 9.81 111.66
> PBTOT -97.24 112.34
> GBSUR -11.57 0.83
> GB 17.69 3.60
> GBSOL 6.12 3.13
> GBELE 14.59 2.31
> GBTOT -92.46 8.31
> TSTRA -13.48 0.00
> TSROT -12.67 0.08
> TSVIB -12.03 9.37
> TSTOT -38.18 9.36
>
> 2/ Did you have any errors or warning messages when you created your
> topology files? Did you use the same radii set for all the prmtops?
>
> Unit Editor: Warning: Close contact of 1.814733 angstroms between .R<R01
> 1>.A<H10 11> and .R<R01 1>.A<H147 17>
> Unit Editor: Warning: Close contact of 1.677883 angstroms between .R<R01
> 1>.A<H30 27> and .R<R01 1>.A<H143 41>
> Unit Editor: Warning: Close contact of 1.781609 angstroms between .R<R01
> 1>.A<H51 51> and .R<R01 1>.A<H167 57>
> Unit Editor: Warning: Close contact of 1.706825 angstroms between .R<R01
> 1>.A<H71 75> and .R<R01 1>.A<H163 81>
> Unit Editor: Warning: Close contact of 1.738386 angstroms between .R<R01
> 1>.A<H91 99> and .R<R01 1>.A<H159 105>
> Unit Editor: Warning: Close contact of 1.817811 angstroms between .R<R01
> 1>.A<H111 123> and .R<R01 1>.A<H155 129>
> Unit Editor: Warning: Close contact of 1.896225 angstroms between .R<R01
> 1>.A<H120 144> and .R<R01 1>.A<H150 166>
> Unit Editor: Warning: Close contact of 1.821769 angstroms between .R<R01
> 1>.A<H123 147> and .R<R01 1>.A<H150 166>
>
> 3/ Did you use the same radii set for all the prmtops?
> How and At what time??
>
>
> > Date: Sat, 7 May 2011 13:21:27 -0400
> > From: brmilleriii.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
> >
> > When you say the delta INT value is not zero, what is it? How far away
> from
> > zero is it? Did you have any errors or warning messages when you created
> > your topology files? Did you use the same radii set for all the prmtops?
> Can
> > you post complex, receptor, ligand, and delta energy values? Did
> > mm_pbsa.plprovide you with any warning or error messaged either?
> >
> > Another suggestion might be to try using MMPBSA.py released with the new
> > AmberTools 1.5. This MM-PBSA script has a lot of error/warning catching
> > messages, particularly in regards to topology inconsistencies that might
> be
> > of use here.
> >
> > I hope that helps.
> >
> > -Bill
> >
> > On Sat, May 7, 2011 at 1:15 PM, mirage . <m.o.m.live.fr> wrote:
> >
> > >
> > > Any Help please
> > >
> > > > From: m.o.m.live.fr
> > > > To: amber.ambermd.org
> > > > Date: Fri, 6 May 2011 08:24:11 +0000
> > > > Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
> > > >
> > > >
> > > > 1) Did you use the single or triple trajectory approach to calculate
> > > binding energy?
> > > > -> Single trajectory
> > > >
> > > > 2) I assume you are talking about the delta INT value, not the
> > > individual INT values
> > > > -> Yes
> > > >
> > > > 3) It is usually easiest to make all the necessary prmtop files at
> the
> > > same time to
> > > > help prevent these types of errors.
> > > > ->I regenerated *.prmtop from *.prep and do mm_pbsa calculation but
> i
> > > found the same INT!!!
> > > >
> > > > 4) This may not be the issue, but without more information this
> problem
> > > is difficult to diagnose
> > > > -> What informations?
> > > >
> > > > > Date: Thu, 5 May 2011 15:31:04 -0400
> > > > > From: dwight.mcgee.gmail.com
> > > > > To: amber.ambermd.org
> > > > > Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
> > > > >
> > > > > Hi,
> > > > >
> > > > > Just to add to what Bill has already stated in the previous email.
> Did
> > > you
> > > > > use the single or triple trajectory approach to calculate binding
> > > energy?
> > > > >
> > > > > On Thu, May 5, 2011 at 3:26 PM, Bill Miller III <
> brmilleriii.gmail.com
> > > >wrote:
> > > > >
> > > > > > I assume you are talking about the delta INT value, not the
> > > individual INT
> > > > > > values. This is often due to inconsistencies in the prmtop files.
> It
> > > is
> > > > > > usually easiest to make all the necessary prmtop files at the
> same
> > > time to
> > > > > > help prevent these types of errors.
> > > > > >
> > > > > > This may not be the issue, but without more information this
> problem
> > > is
> > > > > > difficult to diagnose.
> > > > > >
> > > > > > -Bill
> > > > > >
> > > > > > On Thu, May 5, 2011 at 3:15 PM, mirage . <m.o.m.live.fr> wrote:
> > > > > >
> > > > > > >
> > > > > > > Hi
> > > > > > > The internal energy term INT is not zero, in a single
> trajectory
> > > mm_pbsa
> > > > > > > calculations.
> > > > > > >
> > > > > > >
> > > > > > > What's wrong??
> > > > > > > Thanks in advance for any help
> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Bill Miller III
> > > > > > Quantum Theory Project,
> > > > > > University of Florida
> > > > > > Ph.D. Graduate Student
> > > > > > 352-392-6715
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > T. Dwight McGee Jr.
> > > > > Quantum Theory Project
> > > > > University of Florida
> > > > > Graduate Student
> > > > > 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
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > 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. Candidate
352-392-4032
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Received on Sun May 08 2011 - 02:00:04 PDT
