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

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 10 2008 - 00:18:07 CDT

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/      Fax: 217-244-6078

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