Subject: I'm confused about CHARMM

From: "Dr. Richard Wood" <[email-masked]>
Date: Thu, 15 Feb 2001 16:58:43 -0500

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 @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