VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Mar 17 2008 - 14:48:37 CDT

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.prmtopInfo) Analyzing structure ...Info) Atoms: 134546Info) Bonds: 134745Info) Residues: 38761Info) Waters: 37202Info) Segments: 1Info) Fragments: 37309 Protein: 6 Nucleic: 0dcdplugin) detected standard 32-bit DCD file of native endiannessdcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)Info) Using plugin dcd for coordinates from file h5a2fr.dcdInfo) 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
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