The PRBRAD=1.4 in binding_energy.mmpbsa
> From: m.o.m.live.fr
> To: amber.ambermd.org
> Date: Sun, 8 May 2011 08:43:03 +0000
> Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
>
>
>
>
>
> 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
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> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
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> >
> >
> >
> > --
> > 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
>
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Received on Sun May 08 2011 - 02:00:03 PDT
