Re: Cl and H-bonding (fwd)

From: amber mail account <>
Date: Thu 20 Dec 2001 12:36:58 -0800 (PST)

---------- Forwarded message ----------
Date: Wed, 19 Dec 2001 11:02:36 -0800 (PST)
From: Bill Ross <>
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

Bill Ross
Received on Thu Dec 20 2001 - 12:36:58 PST
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