Tutorial-l Mailing List

From: Michael Bach (mbach_at_ks.uiuc.edu)
Date: Wed Mar 21 2007 - 14:08:23 CDT

---------- Forwarded message ----------
Date: Wed, 21 Mar 2007 14:47:36 -0400
From: Ana Celia Araujo Vila Verde <avilaverde_at_engr.psu.edu>
To: Michael Bach <mbach_at_ks.uiuc.edu>
Subject: RE: tutorial-l: script for hbond time series (fwd)

OK, I just noticed that the script I sent you does not output a time-series of the hbonds... Sorry, it's been a while since I've used it and I got confused. What my script does is to count the HBonds that form at every frame and then output a file containing, for each type of HBond that occurs, the total number of times that that HBond occurred. Typical output looks like this:

GLN:N GLN:OE1 GLN:HN 171 182 172 3

Where:
  - GLN:N means the N atom in one of the GLN residues (donor atom); GLN:OE1 means the OE1 atom in one of the GLN residues (acceptor atom); 1GLN:HN means the HN atom in one of the GLN residues (hydrogen atom).
  - 171 182 172 are the indexes for each of the atoms (donor, acceptor, hydrogen);
  - 3 is the number of HBonds of this type found in the *dcd under study.

Sorry for the mix-up... Maybe this will be useful to you anyway? you can try searching the NAMD list; maybe someone else has a script that does what you need.

Ana

_________________________________
Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA

  <http://www.gfct.fisica.uminho.pt/Members/acvv>
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
avilaverde_at_engr.psu.edu
http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
http://www.gfct.fisica.uminho.pt/Members/acvv
_________________________________

-----Original Message-----
From: owner-tutorial-l_at_ks.uiuc.edu [mailto:owner-tutorial-l_at_ks.uiuc.edu] On Behalf Of Ana Celia Araujo Vila Verde
Sent: Wednesday, March 21, 2007 12:01 PM
To: Michael Bach; tutorial-l_at_ks.uiuc.edu
Subject: RE: tutorial-l: script for hbond time series (fwd)

Try this script. I'm pretty sure it displays general "ickinness" (meaning, it may be written in an inefficient way that shows all I don't know about *tcl), but it does the job. And anyone finding a bug, please do let me know...

Ana

   _____

From: owner-tutorial-l_at_ks.uiuc.edu on behalf of Michael Bach
Sent: Wed 3/21/2007 11:29 AM
To: tutorial-l_at_ks.uiuc.edu
Subject: tutorial-l: script for hbond time series (fwd)

---------- Forwarded message ----------
Date: Wed, 21 Mar 2007 05:00:06 +0100
From: saravana <saravana_at_physik.uni-kl.de>
To: owner-tutorial-l_at_ks.uiuc.edu
Subject: script for hbond time series

Does any body have tcl script for hbond time series of Prot-protein and
Protein-solvent
thanks
regs
sap
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