VMD-L Mailing List

From: alexandra.marques_at_fc.up.pt
Date: Fri Sep 01 2006 - 14:20:35 CDT

Hi

Thanks. My protein is complexed with a ligand and I am interested in identify
waters with long residence times, particularly in the active site, near the
ligand. I thought that one way to do this would be to identify the
waters frame
by frame around the ligand. Do you know if there is an easy or more "correct"
way (or a script...) to identify waters with long residence times across a
trajectory?

Many thanks
Alex

Quoting Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>:

> On 8/31/06, alexandra.marques_at_fc.up.pt <alexandra.marques_at_fc.up.pt> wrote:
>>
>> Hi
>>
>> I still have a problem with my script to write the list of water
>> molecules for
>> each frame. The problem is with the format of the output file, that is, for
>> each frame, the waters are listed in the horizontal and vertical lines. For
>> example:
>>
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>> Frame 0, 4561 4593 4614 4639 5215 5216 5220 7142 7186 7201 8694
>>
>> As my trajectory has 5000 frames the output file is very big and hard to
>> analyse. Does anyone knows how should I modify the script in order to the
>> waters be listed for each frame only in one line?
>> The script is:
>>
>> set outfile [open watersTDT.txt w]
>> set sel [atomselect top "name O and resname WAT and within 3.5 of
>> residue 255"]
>> 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 3.5 of residue 255:"
>> puts "$residuelist"
>
>> foreach res $residuelist {
>> puts $outfile "Frame $i, $residuelist"
>
> why do you output $residuelist here and not $res ??
> this loop is redundant. either write $residuelist once
> or write $res in each line.
>
> i'm also wondering why you need to output this and cannot
> do the subsequent analysis right from withing vmd anyways.
>
> almost anything you could do with an external program you
> can do with tcl as well, and even though tcl is signifiantly slower
> than compiled code, the time needed to write out and then
> read in and parse formatted text is significant, too.
>
> cheers,
> axel.
>
>
>> }
>> }
>> close $outfile
>>
>>
>> Thank you very much for your help
>> Alex
>>
>>
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>>
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>>
>>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

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