I'm confused about CHARMM

["Dr. Richard Wood" <rlw28 at.at cornell.edu>]

Hi all
 I'm still confused about this hydrogen bond thing.
 I can use the COOR DIST cut command in the following way:
 set 1 1
 LABEL LOOP
    TRAJ READ
  COOR DIST cut 3.0    sele segid WAT .and. type H* end -
     sele segid CBHL .and. type O* end
  COOR DIST cut 3.0    sele segid WAT .and. type H* end -
     sele segid CBHL .and. type N* end
  COOR DIST cut 3.0    sele segid WAT .and. type H* end -
     sele segid MANN .and. type O* end
  COOR DIST cut 3.0    sele segid WAT .and. type OH2 end -
     sele segid CBHL .and. type H* end
  COOR DIST cut 3.0    sele segid WAT .and. type OH2 end -
     sele segid MANN .and. type H* end
  COOR DIST cut 3.0    sele segid WAT .and. type OH2 end -
     sele segid WAT .and. type H* end
  COOR DIST cut 3.0    sele segid MANN .and. type O* end -
     sele segid MANN .and. type H* end
 increment 1 by 1
 IF 1 LE  at.at NTOT GOTO LOOP
 to get lists of pairs of "hydrogen bonded" atoms from each 1 ps
 set of a trajectory.
 The last two statements involve waters and sugars and include
 pairs that are in the same molecule and I don't know how to
 make it so that they aren't counted.  In other words, the oxygen and
 hydrogen of an OH group of a sugar, for example, shouldn't be i
 ncluded because they are bonded to each other.
 The thing is, how do I know that any pair of atoms A---H are a
 true hydrogen bond from this type of "calculation"?
 I know that there is an HBONDS command that one can use in DYNAMICS;
 does one have to do this in order to get H-bond information?
 If I try and put a PRINT HBONDS command in an input file, I get a
 message
 that says certain atoms don't have h-bond parameters, in other words the
 parameters are missing.
 Then supposedly there is COOR HBOND, but I don't know a lot about that
 either.
 Still confused about CHARMM
 Richard
 --
 Richard L. Wood, Ph. D.
 Physical/Computational Chemist
 Post-doctoral Associate
 Cornell University, Ithaca, NY 14853