From: Irene Newhouse (
Date: Mon Mar 17 2008 - 15:50:03 CDT

Thanks for your quick response. What I really want to do is to identify all of the waters that are in position to form a "bridging" H bond between the protein & ligand, and to compute the % occupancy of any water in that position. I need to do this analysis because there's such a bridging water in the crystal structure. But in solution the position is dynamic -- if I identify water within a certain distance of the ligand, make that selection & animate, the waters all move far away from the ligand w/in a few steps, as you'd expect. closewater.tcl doesn't do all of that, but I could use results from it to do what I want.
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 normal 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> >> > ________________________________> > Connect and share in new ways with Windows Live. Get it now!
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