> 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 23 2005 - 05:53:01 PST
