Re: [AMBER] regarding per residue wise free energy decomposition

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Tue, 5 Jul 2011 10:56:05 +0530

Hi Bill,
Sorry for delay in reply. I was out of town for a while. I have run the *
Run.mmpbsa.test* script at location (opt/amber10/src/mm_pbsa/Examples/). The
I am sending the generated output file. I have got few failures in that..

Hirdesh

On Wed, Jun 29, 2011 at 4:19 PM, Bill Miller III <brmilleriii.gmail.com>wrote:

> Have you tried running the mm_pbsa.pl tests? There should be a test for
> decomposition in $AMBERHOME/test/mm_pbsa/ or
> $AMBERHOME/src/mm_pbsa/Examples/. Try these to see if they have the same
> problem or if it is something specific to your system.
>
> Also, have you tried the binding energy calculation without decomposition?
> Does that give the same errors?
>
> -Bill
>
> On Mon, Jun 27, 2011 at 1:49 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> >wrote:
>
> > I was not able to upload the files due to file size limitation. So, Here
> I
> > am displaying some of the lines from the snapshot_out files...
> >
> > snapshot_com.all.out
> >
> > MM
> > GB
> > MS
> > GB_SURFTEN 0.0072
> > GB_SURFOFF 0.00
> > 1
> > TDC 1 21.479 -2.079 -70.061 -47.845 0.000
> > TDC 2 19.467 -1.068 -77.642 9.091 0.000
> > TDC 3 15.434 -5.259 -121.855 24.673 0.000
> > TDC 4 22.491 -4.316 -13.125 5.275 0.000
> > TDC 5 15.904 -7.535 -2.917 12.434 0.000
> > TDC 6 22.281 -8.027 -6.336 -4.419 0.000
> > TDC 7 26.854 -9.289 -10.676 15.023 0.000
> > TDC 8 12.247 -4.734 -6.106 -0.275 0.000
> > TDC 9 14.011 -5.779 -9.913 9.142 0.000
> > TDC 10 24.484 -8.312 -10.443 11.079 0.000
> > TDC 11 11.784 -4.080 -10.766 9.945 0.000
> > TDC 12 22.315 -3.694 -97.198 -3.460 0.000
> > TDC 13 19.938 -5.469 -38.873 12.176 0.000
> > TDC 14 26.559 -2.901 -93.548 12.528 0.000
> > TDC 15 9.266 -4.052 -9.742 10.401 0.000
> > TDC 16 20.666 -6.943 -26.012 0.033 0.000
> > TDC 17 6.523 -3.427 -7.071 1.276 0.000
> > TDC 18 24.316 -12.584 -6.398 -11.791 0.000
> > TDC 19 11.205 -4.121 -9.010 3.903 0.000
> > TDC 20 23.244 -6.925 -13.473 10.973 0.000
> > TDC 21 16.120 -5.930 -4.035 9.224 0.000
> > TDC 22 25.195 -9.216 0.090 15.225 0.000
> > TDC 23 20.847 -6.779 -115.447 11.875 0.000
> > TDC 24 21.116 -5.574 -33.419 11.694 0.000
> > TDC 25 18.090 -7.113 -10.931 10.493 0.000
> > TDC 26 23.536 -2.694 29.550 -2.512 0.000
> > TDC 27 25.075 -3.776 -137.682 -1.838 0.000
> > TDC 28 21.699 -0.966 -86.152 -2.647 0.000
> > TDC 29 17.111 -5.130 -23.625 23.696 0.000
> > TDC 30 18.872 -6.558 49.060 -45.485 0.000
> > TDC 31 24.115 -8.954 -16.974 9.294 0.000
> > TDC 32 29.189 -4.474 -15.003 6.754 0.000
> > TDC 33 19.208 -8.218 -8.332 1.256 0.000
> > TDC 34 13.562 -5.723 -9.051 8.822 0.000
> > TDC 35 23.340 -5.434 -11.626 5.181 0.000
> > TDC 36 27.282 -13.774 -2.198 5.417 0.000
> > TDC 37 31.532 -6.708 -4.712 15.083 0.000
> > ...
> > ...
> > ...
> > BDC 326 11.746 -1.037 -3.525 -1.239 0.000
> > BDC 327 11.867 0.030 5.328 -2.543 0.000
> > BDC 328 13.084 0.363 -1.360 -5.850 0.000
> > BDC 329 10.625 -0.720 1.099 -62.283 0.000
> > BDC 330 0.000 0.000 0.000 0.000 0.000
> > BDC 331 0.000 0.000 0.000 0.000 0.000
> >
> >
> >
> >
> > >From snapshot_lig.all.out
> > MM
> > GB
> > MS
> > GB_SURFTEN 0.0072
> > GB_SURFOFF 0.00
> > 1
> > TDC 1 34.278 13.545 -18.005 -13.226 0.000
> > SDC 1 34.278 13.545 -18.005 -13.226 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 2
> > TDC 1 38.119 11.837 -18.003 -13.088 0.000
> > SDC 1 38.119 11.837 -18.003 -13.088 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 3
> > TDC 1 38.104 11.201 -19.595 -12.405 0.000
> > SDC 1 38.104 11.201 -19.595 -12.405 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 4
> > TDC 1 40.842 12.135 -17.259 -13.709 0.000
> > SDC 1 40.842 12.135 -17.259 -13.709 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 5
> > TDC 1 39.196 12.091 -18.432 -13.065 0.000
> > SDC 1 39.196 12.091 -18.432 -13.065 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 6
> > TDC 1 41.053 11.649 -17.915 -13.046 0.000
> > SDC 1 41.053 11.649 -17.915 -13.046 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > ....
> > ....
> > ....
> > TDC 1 49.712 9.334 -19.013 -12.070 0.000
> > SDC 1 49.712 9.334 -19.013 -12.070 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 148
> > TDC 1 35.865 10.625 -18.526 -12.772 0.000
> > SDC 1 35.865 10.625 -18.526 -12.772 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 149
> > TDC 1 31.834 12.854 -17.654 -12.628 0.000
> > SDC 1 31.834 12.854 -17.654 -12.628 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> > 150
> > TDC 1 34.611 10.606 -18.256 -12.783 0.000
> > SDC 1 34.611 10.606 -18.256 -12.783 0.000
> > BDC 1 0.000 0.000 0.000 0.000 0.000
> >
> >
> > >From snapshot_rec.all.out
> > MM
> > GB
> > MS
> > GB_SURFTEN 0.0072
> > GB_SURFOFF 0.00
> > 1
> > TDC 1 21.479 -2.079 -69.853 -47.963 0.000
> > TDC 2 19.467 -1.068 -77.845 9.268 0.000
> > TDC 3 15.434 -5.259 -122.121 24.699 0.000
> > TDC 4 22.491 -4.316 -13.122 5.196 0.000
> > TDC 5 15.904 -7.534 -2.920 12.316 0.000
> > TDC 6 22.281 -8.025 -6.336 -4.191 0.000
> > TDC 7 26.854 -9.284 -10.666 15.287 0.000
> > TDC 8 12.247 -4.727 -6.194 -0.187 0.000
> > TDC 9 14.011 -5.757 -10.016 9.414 0.000
> > TDC 10 24.484 -8.270 -10.364 11.452 0.000
> > TDC 11 11.784 -4.032 -10.577 9.222 0.000
> > TDC 12 22.315 -3.663 -98.319 -0.490 0.000
> > TDC 13 19.938 -5.463 -38.882 11.769 0.000
> > TDC 14 26.559 -2.878 -93.458 12.288 0.000
> > TDC 15 9.266 -4.027 -9.521 10.284 0.000
> > TDC 16 20.666 -6.856 -25.810 0.138 0.000
> > TDC 17 6.523 -3.419 -6.943 0.956 0.000
> > TDC 18 24.316 -12.578 -6.374 -11.472 0.000
> > TDC 19 11.205 -4.119 -8.960 3.718 0.000
> > TDC 20 23.244 -6.922 -13.414 10.842 0.000
> > TDC 21 16.120 -5.929 -4.003 9.094 0.000
> > ...
> > ...
> > ...
> > BDC 313 9.931 -3.113 -8.767 7.162 0.000
> > BDC 314 13.460 -2.412 -9.505 -1.100 0.000
> > BDC 315 12.625 -1.133 -10.824 12.929 0.000
> > BDC 316 11.452 -2.860 -11.239 -5.100 0.000
> > BDC 317 11.294 -1.898 -5.617 7.031 0.000
> > BDC 318 13.510 -0.137 -15.139 -4.734 0.000
> > BDC 319 12.000 -1.423 -11.481 -4.490 0.000
> > BDC 320 9.692 0.522 -7.284 -1.127 0.000
> > BDC 321 9.286 -3.433 -11.256 2.742 0.000
> > BDC 322 12.033 -1.687 -9.590 11.056 0.000
> > BDC 323 12.113 -1.362 -9.335 7.351 0.000
> > BDC 324 15.990 -0.427 -9.831 1.332 0.000
> > BDC 325 10.475 -1.482 -6.481 4.350 0.000
> > BDC 326 11.746 -1.037 -3.521 -1.220 0.000
> > BDC 327 11.867 0.031 5.337 -2.546 0.000
> > BDC 328 13.084 0.363 -1.352 -5.837 0.000
> > BDC 329 10.625 -0.720 1.181 -62.363 0.000
> > BDC 330 0.000 0.000 0.000 0.000 0.000
> >
> > On Fri, Jun 24, 2011 at 6:00 PM, Bill Miller III <brmilleriii.gmail.com
> > >wrote:
> >
> > > What about the energy output files (snapshot_com.all.out,
> > > snapshot_rec.all.out, and snapshot_lig.all.out)? Have you looked at
> > these?
> > > Can you attach those or show the energies from some of the frames from
> > > those
> > > files?
> > >
> > > -Bill
> > >
> > > On Fri, Jun 24, 2011 at 3:59 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> > > >wrote:
> > >
> > > > Hi Bill,
> > > > It is giving only following odd message:
> > > > No values for GB_SGBSOL existing -> Skipping
> > > > No values for GB_BGBSOL existing -> Skipping
> > > >
> > > > The log file is attached for further reference. Please have a look on
> > > that
> > > > as well.
> > > >
> > > > Thanks and Regards,
> > > > Hirdesh Kumar
> > > >
> > > >
> > > > On Fri, Jun 24, 2011 at 2:19 AM, Bill Miller III <
> > brmilleriii.gmail.com
> > > > >wrote:
> > > >
> > > > > What information was printed in the standard out and standard error
> > > > files?
> > > > > Or in your logfile from the calculation? Were there any messages in
> > > there
> > > > > about missing values or anything else to suggest something went
> > wrong?
> > > > >
> > > > > Also, what version of Amber/AmberTools are you using?
> > > > >
> > > > > -Bill
> > > > >
> > > > > On Wed, Jun 22, 2011 at 12:57 AM, Hirdesh Kumar <
> > > hirdesh.iitd.gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Dear All,
> > > > > > This is regarding the per residue decomposition using perl
> script.
> > I
> > > > have
> > > > > > got the output result without any error but the value of non
> polar
> > > > > > solvation
> > > > > > energy term *i.e. *SGBSUR, BGBSUR and TGBSUR* *are zero for
> > protein,
> > > > > > ligand, complex and delta as well.*
> > > > > > *
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Considering the fact that it will affect the true decomposition
> > > > > > contribution, please suggest me the mistake I am doing. Please
> find
> > > the
> > > > > > attached input and output files.
> > > > > >
> > > > > > Thanks and Regards,
> > > > > > Hirdesh Kumar
> > > > > >
> > > > > > _______________________________________________
> > > > > > 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
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
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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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> > 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
>


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Received on Mon Jul 04 2011 - 22:30:04 PDT
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