AMBER Archive (2001)

Subject: Re: Cl and H-bonding (fwd)

From: amber mail account (amber_at_heimdal.compchem.ucsf.edu)
Date: Thu Dec 20 2001 - 14:36:58 CST

---------- Forwarded message ----------
Date: Wed, 19 Dec 2001 11:02:36 -0800 (PST)
From: Bill Ross <ross_at_cgl.ucsf.edu>
To: amber_at_heimdal.compchem.ucsf.edu, christobal_at_angelfire.com
Subject: Re: Cl and H-bonding

        I triing to display H-bonding with Cl or Cl- and I would
        like know there s a way with carnal or ptraj to analyse
        these interactions? Maybe should I define these interactions before?
        
Note the EXACT keyword in carnal's HBOND.

          HBOND hbid [DONOR [EXACT] g1] [ACCEPTOR [EXACT] g2]
                [DISTANCE x] [ANGLE y] [STATS];
              DONOR and ACCEPTOR indicate group ids for searching
              for the appropriate atoms (note: donor is the heavy
              atom to which the hydrogen is attached). The default
              for either is all atoms. A single group id may be
              given in place of separate definitions. If DONOR
              and/or ACCEPTOR are specified, the EXACT option
              forces carnal to use all heavy atoms that may apply,
              instead of just the 'classic' ones such as oxygen and
              nitrogen.

Bill Ross