RE: script for H-bonds extracting

From: Bayly, Christopher <>
Date: Tue 28 Jan 2003 13:40:53 -0500

We use CARNAL to collect H-bond statistics on solvated protein-ligand
compelexes with the following CARNAL input file. The input file is quite
general in terms of any macromolecule and any ligand residue-named LIG; we
use it for running MD simulations in a medium-throughput highly automated
context. H-bonding to waters we exclude on purpose. You might be able to
adapt it to your counting purpose.


     PARM p1 ;
     STREAM s1 mysystem.mdcrd ;
     HBOND hb1 mysystem.donacc LIST ;
     HBOND hb2 mysystem.accdon LIST ;
     GROUP allwat (RES NAME WAT) ;
     GROUP lig (RES NAME LIG) ;
     GROUP non_wat_non_lig ( ! (GROUP allwat) & ! (GROUP lig) ) ;
     HBOND hb1 DONOR non_wat_non_lig ACCEPTOR lig DISTANCE 3.6 STATS;
     HBOND hb2 DONOR lig ACCEPTOR non_wat_non_lig DISTANCE 3.6 STATS;

-----Original Message-----
From: Bimo Ario Tejo []
Sent: Tuesday, January 28, 2003 5:01 AM
Subject: script for H-bonds extracting

Dear Amber users,

I'd like to know does anybody have a script to extract number of H-bond from
CARNAL? What I'm looking for is a script which can give the number of H-bond
from each frames of trajectory, so I can plot the number of H-bond versus
time. To do it manually from .lis file is very tiring job...:-)

Thanks in advance.


Now with e-mail forwarding for only US$5.95/yr
Powered by Outblaze
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named in this message.  If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.
Received on Tue Jan 28 2003 - 10:40:53 PST
Custom Search