VMD-L Mailing List

From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Wed May 07 2008 - 15:52:47 CDT

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