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From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 28 2006 - 11:33:18 CDT
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Hi,
Oops, too late.. (I usually read my emails in order of receipt...)
I'm glad you solved the first part of your problem.
The missing close brace belongs right before your "close $outfile" call.
John Stone
vmd_at_ks.uiuc.edu
On Mon, Aug 28, 2006 at 04:52:03PM +0100, alexandra.marques_at_fc.up.pt wrote:
> 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
> >
> >
> >
> >-------------------------------------------------------------
> >A FCUP utiliza o sistema de webmail Horde/IMP (www.horde.org)
> >
> >Visite: http://www.fc.up.pt/
> >
> >
>
>
>
> -------------------------------------------------------------
> A FCUP utiliza o sistema de webmail Horde/IMP (www.horde.org)
>
> Visite: http://www.fc.up.pt/
>
>
-- 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 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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