AMBER Archive (2005)

Subject: Re: AMBER: carnal - water-mediated HBond

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Jan 22 2005 - 22:49:09 CST

> I have a question on calculating hydrogen bonds using carnal.
> Is there any way to get the list of all possible HBs including the
> water-mediated ones?

What does water-mediated mean? From the manual:

  HBOND hbid [DONOR [EXACT] g1] [ACCEPTOR [EXACT] g2]
        [DISTANCE x] [ANGLE y] [STATS];

  'hbid' is an id from FILES_OUT, above.
  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.**

Looking back up at FILES_OUT / HBOND:

  HBOND hbid base_file [TABLE] [LIST];

  TABLE Output table of occupancies in base_file.tab. This table has two
  sections. The first part is a key that lists the possible hbonds in
  order. The format is:

  # 1 (ADE 2 O5' )--(HB 1 H ) .. (ADE 2 O1' )
  # 2 (ADE 2 O5' )--(HB 1 H ) .. (ADE 2 N7 )

  The second part consists of a matrix of 0's and 1's. Each column is for
  a given hbond pair according to the numbering in the key section, and
  each row (line) is for a coordinate set. The format is '0' if no hbond
  is happening, '1' if it is.

Bill
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