VMD-L Mailing List

From: yzliu (nk.liuyz_at_gmail.com)
Date: Fri Jul 10 2009 - 08:12:23 CDT

Dear all:

    The SASA of a atomselect could be calculated by the "measure"
 command in VMD as follow:
            *"measure sasa srad selection [-restrict restrictedsel] "*
 I do not understand what is the meaning of '-restrict' option exactly.
 In my vmd srcipt as follow, the SASA with the "-restrict"is invariable
 as a funtion of time.

 set nf [molinfo top get numframes]
 set all [atomselect top all]
 set sel [atomselect top "resid 1 and segname DMPC"]

 for {set i 0} {$i < $nf} {incr i} {
    $sel frame $i
    set sasa [measure sasa 1.4 $all -restrict $sel]
    puts $sasa
 }
  I do not know whether there is someting wrong in the script. However, when
 I use "measure sasa 1.4 $sel ", the SASA is changed as evolution.
 In my opinion, without "-restrict" means calculating SASA of a isolated
molecule
 in the solvent.Wiht "-restrict" means calculating SASA of a molecule in the

 real environment. The diffierent circumstance would influence the SASA.

 I am not sure whether my understanding is right.
 Any information will be appreciaed

 Best Regards,

 Yingzhe 

-- 
==============================
Yingzhe Liu
PHD Student of Analytical Chemistry
Chemistry Department
Nankai University
Tianjin, P.R.China,30071
Email: nk.liuyz_at_gmail.com
==============================