VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 07 2008 - 16:59:55 CDT

Hi,
  Which version of VMD are you using?
You should definitely be using more than 50 samples, that is far
too low for accurate results, normally one would use 500 or more.

Another question is whether you're using exactly the same structures
in your comparisons. Are you loading a single structure
(e.g. PDB) or are you loading a trajectory? Be sure you're comparing
identical frames etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 07, 2008 at 04:52:47PM -0400, Jufang Shan wrote:
> Hi,
>
> I have been using the same script to calculate sasa on different machines
> (platforms) but got different results. I was wondering has anyone encounter
> similar problems before.
> For some residues, the difference is bigger; for some, small.
>
> Here is the sasa-calculation script:
> set sel [atomselect top "protein or lipids"]
> set surf [atomselect top "segid A2 and resid 342"]
> set sasa [measure sasa 1.4 $sel -points pts -restrict $surf]
> #set sasa [measure sasa 1.4 $sel -points pts -restrict $surf -samples 50]
>
> Here is the result if I turn off flag "-samples 50". x86_64 gives the same
> result as ia64.
> PC: 21.49
> ia64: 17.77
> irix:18.39
>
> The result is still different when I change the probe to 1.0
> PC: 29.3
> ia64:24.5
> irix: 25.7
>
> The result is also different when I use flag "-samples 50"
> PC: 26.94
> ia64: 13.39
> iris:25.47
>
>
> Best,
> Jufang 

-- 
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
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