Re: Different Hbonds values on different machines using same script for same trajectories

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 11 2008 - 03:11:11 CDT

Sunita,
  If you're not able to reproduce the erroneous results after many
attempts, then it's possible there's a latent bug in your scripts,
or that you may have made a mistake during the initial runs that
you reported previously and they weren't actually identical
calculations. Anyway, I don't have any suggestions beyond
what I said previously, just keep checking over the code and
make sure there's not a bug hiding in your script somewhere...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 11, 2008 at 01:30:52PM +0530, sunita gupta wrote:
> hello john,
> ya in both cases I am using vmd version 1.8.6.....and running on windows
> platform of both machines.I am having only 1 .dcd file concatenated by
> catdcd...and loading them in same order in both the cases after loading .psf
> files.
> as per your suggestion i made a little change in the hbonds.tcl
> script....and ran it on both machines....now its giving exactly the same
> output....
> more interesting thing i found is that....now when i ran the original
> script...(ie.the script without any changes...that i was using
> earlier).....on both machines.....using same parameters....
> surprisingly i am getting exactly same results.....:)
> what might be the reason.....?i am not able 2 understand.
> Thanks
>
>
>
>
>
>
> On Tue, Jun 10, 2008 at 10:48 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > Without going in and reading your scripts in detail, I think there
> > are several likely answers to your question. First, I'm assuming that
> > in all cases you're using the same version of VMD, and you're running
> > on the same type of machine (e.g. linux on x86 for both tests, let's say).
> >
> > If the assumption above is the case, then the most likely reason for
> > getting varying results is due to variation in the input, in terms of
> > the order that you loaded files, and/or whether you loaded the trajectory
> > with a structure file like a PDB, versus loading it with a PSF, and/or
> > whether you loaded the files in a different order, as that can have an
> > effect on the list of bonds given to VMD, and as the bonds are held
> > fixed throughout a trajectory, any difference in initial bonding could
> > potential have an effect on your results since the "measure hbonds" code
> > would process somewhat different candidate atoms.
> >
> > Another possibility is that there's a bug in your GUI/scripts that's
> > resulted in having a variation in the input to "measure hbonds" from
> > one run to the next. To eliminate this possibility, I'd add some extra
> > "puts" calls in your code so you can see what is being sent in to
> > the "measure hbonds" command and record/compare those values as well
> > as the output.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Mon, Jun 09, 2008 at 12:59:57PM +0530, sunita gupta wrote:
> > > Hello All
> > >
> > > I wonder I am getting different Hbonds values when calculating on
> > different
> > > machines for the same trajectories , using same script....hbonds.tcl
> > (taken
> > > from mailing list)
> > > all the three files are attached with this mail.naming hbond1.txt ,
> > > hbond2.txt, and hbonds.tcl
> > > Any help will be highly appreciated...
> > >
> > > Thanks
> > >
> > > --
> > > SUNITA GUPTA
> > > Member Research Team
> > > Lead Invent Technology
> > > TBIU, IIT Delhi, India
> > > Email- sunita_at_leadinvent.com
> > > Ph- +9111 26581524 (Ex-6)
> >
> >
> > > Mon Jun 09 12:33:27 PM India Standard Time 2008 Search start.
> > > *****25*****50*****75*****100*
> > > Mon Jun 09 12:33:45 PM India Standard Time 2008 Search finished.
> > > Find 93 hbonds.
> > > donor acceptor occupancy
> > > ChainB-ASN183-Side ChainC-GUA15-Side 15.88%
> > > ChainB-THR180-Side ChainC-GUA14-Side 0.46%
> > > ChainB-VAL177-Main ChainC-GUA14-Side 0.31%
> > > ChainB-GLN153-Side ChainC-GUA13-Side 0.31%
> > > ChainB-TYR184-Side ChainC-GUA13-Side 7.48%
> > > ChainB-ASN167-Main ChainD-ADE22-Side 0.31%
> > > ChainA-ASN167-Main ChainC-ADE22-Side 0.92%
> > > ChainA-ASN167-Side ChainC-GUA23-Side 2.60%
> > > ChainA-LYS179-Side ChainD-GUA16-Side 16.34%
> > > ChainA-LYS179-Side ChainD-GUA15-Side 39.24%
> > > ChainA-VAL177-Main ChainD-GUA14-Side 0.61%
> > > ChainA-THR180-Side ChainD-GUA14-Side 9.16%
> > > ChainB-LYS179-Side ChainC-GUA15-Side 9.16%
> > > ChainB-LYS179-Side ChainC-GUA16-Side 24.73%
> > > ChainB-SER186-Side ChainD-THY24-Side 0.31%
> > > ChainB-ASN167-Side ChainD-GUA23-Side 0.31%
> > > ChainB-ARG197-Main ChainD-GUA23-Side 0.15%
> > > ChainA-TYR184-Side ChainD-ADE13-Side 8.09%
> > > ChainA-ASN183-Side ChainD-GUA15-Side 25.19%
> > > ChainA-ARG197-Side ChainC-GUA23-Side 6.56%
> > > ChainA-GLN153-Side ChainD-ADE13-Side 5.34%
> > > ChainA-SER186-Side ChainC-THY24-Side 1.98%
> > > ChainB-LYS182-Side ChainD-ADE22-Side 7.18%
> > > ChainB-ARG196-Side ChainD-GUA23-Side 0.76%
> > > ChainA-SER186-Side ChainC-GUA23-Side 1.83%
> > > ChainB-LYS182-Side ChainD-GUA23-Side 24.43%
> > > ChainA-LYS182-Side ChainC-GUA23-Side 19.85%
> > > ChainA-VAL177-Side ChainD-GUA15-Side 3.97%
> > > ChainA-LEU176-Side ChainD-GUA14-Side 4.27%
> > > ChainA-THR151-Side ChainD-THY12-Side 4.89%
> > > ChainA-GLN153-Side ChainD-THY12-Side 8.85%
> > > ChainA-THR166-Side ChainC-ADE22-Side 5.65%
> > > ChainA-VAL177-Side ChainD-GUA14-Side 7.79%
> > > ChainA-LYS182-Side ChainC-ADE22-Side 2.29%
> > > ChainA-LEU176-Side ChainD-ADE13-Side 6.87%
> > > ChainB-VAL185-Side ChainD-GUA23-Side 3.51%
> > > ChainA-THR166-Side ChainC-ADE21-Side 0.76%
> > > ChainB-ARG187-Side ChainC-GUA14-Side 1.22%
> > > ChainB-TYR184-Side ChainC-THY12-Side 2.44%
> > > ChainB-SER186-Side ChainD-GUA23-Side 7.48%
> > > ChainB-LEU189-Side ChainD-GUA23-Side 1.68%
> > > ChainA-THR180-Side ChainD-ADE13-Side 8.09%
> > > ChainA-MET174-Side ChainD-ADE13-Side 2.90%
> > > ChainB-THR166-Side ChainD-THY21-Side 4.58%
> > > ChainB-ASN167-Side ChainD-ADE22-Side 11.91%
> > > ChainB-ARG196-Side ChainC-ADE20-Side 0.15%
> > > ChainB-THR198-Side ChainC-ADE22-Side 0.31%
> > > ChainB-ARG196-Side ChainC-ADE21-Side 1.83%
> > > ChainA-THR151-Side ChainD-THY11-Side 3.97%
> > > ChainB-GLN153-Side ChainC-THY12-Side 1.37%
> > > ChainB-ASN183-Side ChainC-GUA14-Side 0.46%
> > > ChainB-ALA190-Side ChainD-THY24-Side 0.31%
> > > ChainA-ARG197-Side ChainC-ADE22-Side 1.53%
> > > ChainB-ARG196-Side ChainC-ADE22-Side 4.12%
> > > ChainB-ARG197-Side ChainD-GUA23-Side 3.51%
> > > ChainB-ARG187-Side ChainC-GUA13-Side 25.95%
> > > ChainA-LYS179-Side ChainC-THY24-Side 0.31%
> > > ChainB-LYS168-Side ChainD-THY21-Side 12.21%
> > > ChainA-LYS191-Side ChainD-THY12-Side 0.15%
> > > ChainA-ASN183-Side ChainD-GUA14-Side 1.22%
> > > ChainB-ARG197-Side ChainD-ADE22-Side 2.60%
> > > ChainB-LYS168-Side ChainD-THY20-Side 0.15%
> > > ChainB-LEU189-Side ChainD-ADE22-Side 0.15%
> > > ChainA-ASN167-Side ChainC-ADE22-Side 0.15%
> > > ChainA-LYS191-Side ChainD-THY11-Side 0.92%
> > > ChainA-GLU154-Side ChainD-THY12-Side 0.31%
> > > ChainA-TYR184-Side ChainD-THY12-Side 7.18%
> > > ChainA-ARG196-Side ChainC-GUA23-Side 0.76%
> > > ChainA-ARG187-Side ChainD-THY12-Side 0.15%
> > > ChainA-ARG187-Side ChainD-GUA14-Side 0.15%
> > > ChainA-ARG187-Side ChainD-ADE13-Side 0.15%
> > > ChainA-THR180-Side ChainD-THY12-Side 2.29%
> > > ChainA-VAL177-Side ChainD-ADE13-Side 4.12%
> > > ChainA-LEU176-Side ChainD-THY12-Side 5.34%
> > > ChainA-ARG187-Side ChainD-THY11-Side 1.37%
> > > ChainA-TYR184-Side ChainD-THY11-Side 0.46%
> > > ChainB-LYS168-Side ChainD-ADE22-Side 0.15%
> > > ChainA-ALA171-Side ChainD-ADE13-Side 0.31%
> > > ChainB-GLU178-Side ChainD-ADE22-Side 0.31%
> > > ChainA-MET174-Side ChainD-THY12-Side 0.61%
> > > ChainA-GLN153-Side ChainD-THY11-Side 1.98%
> > > ChainB-ASN167-Side ChainD-THY21-Side 1.68%
> > > ChainA-THR151-Side ChainD-GUA10-Side 1.53%
> > > ChainA-ASP152-Side ChainD-THY11-Side 0.76%
> > > ChainA-LEU189-Side ChainC-THY24-Side 1.07%
> > > ChainA-ARG155-Side ChainD-THY11-Side 0.15%
> > > ChainA-ALA190-Side ChainC-CYT25-Side 0.46%
> > > ChainA-ASP152-Side ChainD-THY12-Side 0.46%
> > > ChainB-ILE170-Side ChainD-ADE22-Side 0.15%
> > > ChainA-LYS179-Side ChainD-GUA14-Side 0.15%
> > > ChainA-LEU189-Side ChainC-GUA23-Side 2.14%
> > > ChainB-VAL177-Side ChainC-GUA14-Side 1.37%
> > > ChainB-THR166-Side ChainD-ADE22-Side 0.31%
> >
> > > Mon Jun 09 12:37:43 PM India Standard Time 2008 Search start.
> > > *****25*****50*****75*****100*
> > > Mon Jun 09 12:38:20 PM India Standard Time 2008 Search finished.
> > > Find 55 hbonds.
> > > donor acceptor occupancy
> > > ChainB-ASN183-Side ChainC-GUA15-Side 15.88%
> > > ChainB-THR180-Side ChainC-GUA14-Side 83.05%
> > > ChainB-VAL177-Main ChainC-GUA14-Side 43.21%
> > > ChainB-GLN153-Side ChainC-GUA13-Side 1.98%
> > > ChainB-TYR184-Side ChainC-GUA13-Side 11.45%
> > > ChainB-ASN167-Main ChainD-ADE22-Side 72.67%
> > > ChainA-ASN167-Main ChainC-ADE22-Side 43.97%
> > > ChainA-ASN167-Side ChainC-GUA23-Side 6.56%
> > > ChainA-LYS179-Side ChainD-GUA16-Side 16.18%
> > > ChainA-LYS179-Side ChainD-GUA15-Side 39.24%
> > > ChainA-VAL177-Main ChainD-GUA14-Side 60.92%
> > > ChainA-THR180-Side ChainD-GUA14-Side 80.61%
> > > ChainB-LYS179-Side ChainC-GUA15-Side 9.16%
> > > ChainB-LYS179-Side ChainC-GUA16-Side 24.73%
> > > ChainB-ASN167-Side ChainD-GUA23-Side 0.31%
> > > ChainB-ARG197-Main ChainD-GUA23-Side 53.89%
> > > ChainA-TYR184-Side ChainD-ADE13-Side 61.07%
> > > ChainA-ASN183-Side ChainD-GUA15-Side 25.19%
> > > ChainA-SER186-Side ChainC-THY24-Side 50.69%
> > > ChainB-SER186-Side ChainD-THY24-Side 54.66%
> > > ChainA-GLN153-Side ChainD-ADE13-Side 24.27%
> > > ChainB-ARG196-Side ChainC-ADE21-Side 0.15%
> > > ChainB-THR166-Side ChainD-ADE22-Side 0.15%
> > > ChainB-ARG197-Side ChainD-GUA23-Side 28.09%
> > > ChainB-LYS182-Side ChainD-ADE22-Side 1.68%
> > > ChainA-SER186-Side ChainC-GUA23-Side 1.83%
> > > ChainB-LYS182-Side ChainD-GUA23-Side 23.51%
> > > ChainA-LYS182-Side ChainC-GUA23-Side 19.85%
> > > ChainA-ARG197-Main ChainC-GUA23-Side 17.71%
> > > ChainA-THR166-Side ChainC-ADE22-Side 0.31%
> > > ChainB-ARG196-Side ChainD-GUA23-Side 1.37%
> > > ChainA-ARG197-Side ChainC-ADE22-Side 0.76%
> > > ChainA-ARG197-Side ChainC-GUA23-Side 52.98%
> > > ChainA-LYS182-Side ChainC-ADE22-Side 2.29%
> > > ChainB-THR166-Main ChainD-ADE22-Side 0.61%
> > > ChainB-ARG187-Side ChainC-GUA14-Side 1.22%
> > > ChainB-TYR184-Side ChainC-THY12-Side 3.51%
> > > ChainA-ARG196-Side ChainD-THY21-Side 1.83%
> > > ChainB-GLN153-Side ChainC-THY12-Side 11.60%
> > > ChainB-ASN183-Side ChainC-GUA14-Side 0.46%
> > > ChainB-ARG197-Side ChainD-ADE22-Side 2.90%
> > > ChainA-THR151-Side ChainD-THY12-Side 1.37%
> > > ChainB-ARG187-Side ChainC-GUA13-Side 25.95%
> > > ChainA-LYS179-Side ChainC-THY24-Side 0.31%
> > > ChainA-ASN183-Side ChainD-GUA14-Side 1.22%
> > > ChainA-ASN167-Side ChainC-ADE22-Side 0.46%
> > > ChainA-LYS168-Side ChainC-ADE21-Side 30.69%
> > > ChainB-LYS168-Side ChainD-THY21-Side 8.40%
> > > ChainA-ARG187-Side ChainD-GUA14-Side 0.15%
> > > ChainA-ARG187-Side ChainD-ADE13-Side 0.15%
> > > ChainB-VAL177-Side ChainC-GUA14-Side 0.15%
> > > ChainA-VAL177-Side ChainD-GUA15-Side 0.15%
> > > ChainB-THR151-Side ChainC-THY12-Side 5.04%
> > > ChainA-LEU189-Side ChainC-GUA23-Side 0.15%
> > > ChainB-THR166-Side ChainD-THY21-Side 0.31%
> >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> >
>
>
>
> --
> SUNITA GUPTA
> Member Research Team
> Lead Invent Technology
> TBIU, IIT Delhi, India
> Email- sunita_at_leadinvent.com
> Ph- +9111 26581524 (Ex-6)

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

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