From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Mar 17 2008 - 15:41:14 CDT

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 <einew_at_hotmail.com> 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) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> 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!