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
> > > > _______________________________________________
> > > > 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
>
--
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
Received on Wed Jun 29 2011 - 04:00:03 PDT
