VMD-L Mailing List

From: alexandra.marques_at_fc.up.pt
Date: Mon Aug 28 2006 - 10:52:03 CDT

Hi again

Sorry, forget my previous mail. I was using a wrong pdb file...
I have another question related with this script. I want to change it to write
the list of waters molecules for each frame, instead of writing a pdb file for
each frame. My modified script is:

set outfile [open waters.txt w]
set sel [atomselect top "name O and resname WAT and within 2 of residue 0"]
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
$sel frame $i
$sel update
set residuelist [$sel get residue]
puts "list of waters within 2 of residue 0:"
puts "$residuelist"
foreach res $residuelist {
puts $outfile "Frame $i, $residuelist"
}
close $outfile

However something is wrong as I am having the following error: missing
close-brace. As I donīt know too much about tcl scripting, could someone
please
take a look and tell me what am I doing wrong?

Thanks!
Alex

Quoting alexandra.marques_at_fc.up.pt:

> Hi
>
> I want to identify the water molecules within 2 angstroms of certain residues
> for each frame of a trajectory. I am using the following script:
>
> set sel [atomselect top "name O and resname WAT and within 2 of residue 0"]
> set n [molinfo top get numframes]
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> $sel update
> $sel writepdb water_$i.pdb
> }
>
> However I am having problems with the numbering of the waters. For
> instance, for
> residue 0 and frame 0 I obtain one water molecule with the number X1546.
> However, If I apply the same script only to the pdb file corresponding to the
> frame 0, the same water molecule is now numbered 910, which is correct. It
> seems that the water molecules in the trajectory are being wrongly
> numbered...
>
> What am I doing wrong? Is there any other simple way to do this type of
> analysis? My trajectory is from amber.
>
>
> Thanks in advance
> Alexandra
>
>
>
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