AMBER Archive (2003)

Subject: RE: script for H-bonds extracting

From: Bayly, Christopher (christopher_bayly_at_merck.com)
Date: Tue Jan 28 2003 - 12:40:53 CST

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.

Christopher

   FILES_IN
     PARM p1 mysystem.top ;
     STREAM s1 mysystem.mdcrd ;
   FILES_OUT
     HBOND hb1 mysystem.donacc LIST ;
     HBOND hb2 mysystem.accdon LIST ;
   DECLARE
     GROUP allwat (RES NAME WAT) ;
     GROUP lig (RES NAME LIG) ;
     GROUP non_wat_non_lig ( ! (GROUP allwat) & ! (GROUP lig) ) ;
   OUTPUT
     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;
   END

-----Original Message-----
From: Bimo Ario Tejo [mailto:bimo7_at_linuxmail.org]
Sent: Tuesday, January 28, 2003 5:01 AM
To: amber_at_heimdal.compchem.ucsf.edu
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.

Bimo 

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