VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 21 2012 - 14:31:09 CST

Hi,
  You didn't say "how different" your PDB results were, but they will
not be identical to the results you get from doing the calculation using
the trajectory simply because PDB files store the atom coordinates with
much lower precision than the trajectory files to, so the SASA calculations
will thus give different results. I would expect the percent deviation of
the two results to be minor, but it will definitely be noticable.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 21, 2012 at 06:36:07PM +0000, Ban Arn wrote:
> Dear VMD users
>
> I am using the following script to SASA calculation.
>
> # solvent accessible surface area calculation through the trajectory
> # compare chain D with others
> # loading trajectory
>
> # setup binding site 7A
> set binding_site [atomselect 0 "protein within 6 of resname UNK"]
>
> # load atoms* radii information (same as used in DSSP)
> [atomselect top "name O"] set radius 1.40
> [atomselect top "name N"] set radius 1.65
> [atomselect top "name CA"] set radius 1.87
> [atomselect top "name C"] set radius 1.76
> [atomselect top "noh and not name O N CA C"] set radius 1.80
> [atomselect top "hydrogen"] set radius 0.0
>
> # start procedure (function)
> proc sasa_trj { sel file } {
> # open file for writing
> set fout [open $file w]
> # get molecule*s ID from the selection of function arguments
> set molid [$sel molid]
> # get the number of frames of loaded trajectory
> set nf [molinfo $molid get numframes]
> # measure for all five subunits
> set protein [atomselect $molid "protein and noh"]
> # select a residue from each subunit
> set s1 [atomselect $molid "[$sel text]"]
>
> for { set i 0 } { $i < $nf } { incr i } {
> # frame (trajectory) update corresponding selections
> molinfo $molid set frame $i
> $protein frame $i
> $sel frame $i
> $s1 frame $i
>
> # consider the whole protein but calculate for
> #the subunit with probe solvent radius of 1.4 A
> set sa1 [measure sasa 1.40 $protein -restrict $s1]
>
> # print out (time average_of_four_subunits orange_subunit)
> puts $fout "[expr $i*0.01] $sa1"
> }
> close $fout
> }
>
> I would like to conform that the script updates the each frames for the
> selection.
>
> I tried for intermediate frames in the trajectory by saving them as pdb,
> the results are different.
>
> If the script doesn't update for every frame, kindly advice how to modify
> the script.
>
> Many Thanks
> Balaji 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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