From: Axel Kohlmeyer (
Date: Mon Mar 17 2008 - 16:02:02 CDT

On Mon, 17 Mar 2008, Irene Newhouse wrote:



IN> Thanks for your quick response. What I really want to do is to
IN> identify all of the waters that are in position to form a "bridging"
IN> H bond between the protein & ligand, and to compute the % occupancy
IN> of any water in that position. I need to do this analysis because
IN> there's such a bridging water in the crystal structure. But in
IN> solution the position is dynamic -- if I identify water within a
IN> certain distance of the ligand, make that selection & animate, the
IN> waters all move far away from the ligand w/in a few steps, as you'd

you have to activate the "Update Selection Every Frame" flag
in the Trajectory tab of the representation to have the
selection re-evaluated in every frame. and if you build a
selection that looks for water oxygens exwithin a given distance
of the ligand _and_ exwithin a given distance of the protein
you should get already pretty close to what you want.

you can also script this rather easily using one of the
"loop over all frames" script templates and then just
use the selection and do
$sel frame $i
$sel update

print "$i [$sel num]"

to get the numbers per frame.

IN> expect. closewater.tcl doesn't do all of that, but I could use
IN> results from it to do what I want.

closewater looks like overkill to me.
the trick for good performance is always to restrict
a selection text the most with the first statement.


IN> Irene> Date: Mon, 17 Mar 2008 15:41:14 -0500> From:> To:> Subject: Re: vmd-l: closewater.tcl> CC:> > Hi Irene,> > If you want to count the number of waters around your solute, I have a> script that does the work.> > Cheers,> Michel> > On Mon, Mar 17, 2008 at 2:48 PM, Irene Newhouse <> wrote:> >> > I'm trying to identify bridging waters between a protein & a glycan ligand.> > It's a large system. I searched through the VMD archive. I wasn't able to> > figure out from the material deposited how to use the bridging water script,> > so I looked some more & found the closewater script, which almost does what> > I want. But I can't get it to complete, even when I select, as a trial, only> > 2 frames out of a dcd file. I've given it 40 minutes of cpu time on a linux> > cluster. There are no new files, and this is the only output so far:> >> >> >> >> >> > Info) VMD for LINUXAMD64, version 1.8.6 (April 6!
 , 2007)> > Info)> > Info) Email questions and bug reports to> > Info) Please include this reference in published work using VMD:> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.> > Info) -------------------------------------------------------------> > Info) Multithreading available, 4 CPUs detected.> > Info) Free system memory: 5088MB (63%)> > Info) Using plugin parm7 for structure file h5a2fr.prmtop> > Info) Analyzing structure ...> > Info) Atoms: 134546> > Info) Bonds: 134745> > Info) Residues: 38761> > Info) Waters: 37202> > Info) Segments: 1> > Info) Fragments: 37309 Protein: 6 Nucleic: 0> > dcdplugin) detected standard 32-bit DCD file of native endianness> > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)> > Info) Using plugin dcd for coordinates from file h5a2fr.dcd> > Info) Finished with coordinate file h5a2fr.dcd.> > 0!
> >> >> >> > I recognize that everything but the last line is the norm
al initial VMD> > output.> >> >> >> >> > I did find that, in the script as downloaded, "num" could not be assigned> > from the current version of VMD. Therefore I commented out the one loop that> > uses it - it's error detection to make sure you're not trying to identify> > more waters than the system contains. That's not a problem here - no one in> > their right mind would think of that many waters as 'close'. [I'm trying to> > do the 5 closest waters, by the way]. Then I found that I couldn't figure> > out how to delimit the atom selection in the input line [spaces...] So> > rather than keep on trying, I just hard-wired that in for the time being.> >> >> >> > I suspect that I've run into yet another incompatibility between closewater> > & 'my' version of VMD - 1.8.6 - but I'm not seeing it.> >> >> >> >> > Has someone recently worked successfully with closewater? What is the 0> > trying to tell me?> >> >> >> >> >> > Thanks for any help!> >> >> >> >> >> > Irene Newhouse> >> !
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Axel Kohlmeyer
   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.