With the python version i obtain :
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR DIHED).
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 129.9928 1.2577 0.7261
ANGLE 370.4721 5.1930 2.9982
DIHED 534.4306 4.1539 2.3982
VDWAALS -230.9418 4.7870 2.7638
EEL -1147.8563 6.4572 3.7280
EGB -156.6093 5.3742 3.1028
ESURF 24.3822 0.4322 0.2495
G gas -343.9027 6.8927 3.9795
G solv -132.2271 4.9959 2.8844
TOTAL -476.1298 2.0428 1.1794
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 112.6997 0.8750 0.5052
ANGLE 293.4259 4.5350 2.6183
DIHED 480.8591 6.0903 3.5162
VDWAALS -163.7737 5.5598 3.2100
EEL -1091.2657 5.8704 3.3893
EGB -149.7918 4.2735 2.4673
ESURF 20.8926 0.4150 0.2396
G gas -368.0547 11.5631 6.6759
G solv -128.8992 3.8636 2.2307
TOTAL -496.9539 7.7574 4.4787
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 17.2931 0.4062 0.2345
ANGLE 77.0461 2.8233 1.6300
DIHED 59.6612 4.8438 2.7966
VDWAALS -5.6770 1.0886 0.6285
EEL -57.4356 0.6380 0.3684
EGB -15.5414 0.6693 0.3864
ESURF 9.1057 0.0456 0.0264
G gas 90.8878 4.7402 2.7367
G solv -6.4356 0.7067 0.4080
TOTAL 84.4521 5.4182 3.1282
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000 0.0000
ANGLE 0.0000 0.0001 0.0000
DIHED -6.0897 0.1418 0.0819
VDWAALS -61.4911 2.0248 1.1690
EEL 0.8450 0.5068 0.2926
EGB 8.7239 0.9690 0.5595
ESURF -5.6161 0.2068 0.1194
DELTA G gas -66.7357 1.7745 1.0245
DELTA G solv 3.1077 0.7992 0.4614
DELTA G binding = -63.6280 +/- 1.4493 0.8367
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR DIHED).
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 129.9928 1.2577 0.7261
ANGLE 370.4721 5.1930 2.9982
DIHED 534.4306 4.1539 2.3982
VDWAALS -230.9418 4.7870 2.7638
EEL -1147.8563 6.4572 3.7280
EPB -189.3587 7.9210 4.5732
ECAVITY 21.7804 0.1315 0.0759
G gas -343.9027 6.8927 3.9795
G solv -167.5783 7.8153 4.5122
TOTAL -511.4809 1.6325 0.9425
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 112.6997 0.8750 0.5052
ANGLE 293.4259 4.5350 2.6183
DIHED 480.8591 6.0903 3.5162
VDWAALS -163.7737 5.5598 3.2100
EEL -1091.2657 5.8704 3.3893
EPB -186.2662 5.9305 3.4240
ECAVITY 20.9624 0.1877 0.1084
G gas -368.0547 11.5631 6.6759
G solv -165.3038 5.7509 3.3203
TOTAL -533.3585 5.8822 3.3961
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 17.2931 0.4062 0.2345
ANGLE 77.0461 2.8233 1.6300
DIHED 59.6612 4.8438 2.7966
VDWAALS -5.6770 1.0886 0.6285
EEL -57.4356 0.6380 0.3684
EPB -17.2791 1.2607 0.7279
ECAVITY 6.9374 0.0497 0.0287
G gas 90.8878 4.7402 2.7367
G solv -10.3417 1.3071 0.7546
TOTAL 80.5461 5.9751 3.4497
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000 0.0000
ANGLE 0.0000 0.0001 0.0000
DIHED -6.0897 0.1418 0.0819
VDWAALS -61.4911 2.0248 1.1690
EEL 0.8450 0.5068 0.2926
EPB 14.1866 0.7309 0.4220
ECAVITY -6.1194 0.1192 0.0688
DELTA G gas -66.7357 1.7745 1.0245
DELTA G solv 8.0672 0.7623 0.4401
DELTA G binding = -58.6685 +/- 2.1340 1.2321
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
the input is:
Input file for running entropy calculations using NMode
&general
startframe=1,
endframe=3,
# entropy=1,
receptor_mask= ":1,:2,4",
ligand_mask= ":3",
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
~
> From: m.o.m.live.fr
> To: amber.ambermd.org
> Date: Sun, 8 May 2011 08:56:16 +0000
> Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
>
>
> 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
> > > > > > > > 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
>
> _______________________________________________
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Received on Sun May 08 2011 - 03:00:03 PDT
