Given that a hydrogen bond is considered present when the distance between donor-acceptor is 2.4 Å, one can either look at it manually using a graphical program (e.g. RASMOL or a similar free software), or submit the structure to the WHATIF/PROCHECK structure analysis site on the web.
If you want to do it in CHARMM, the syntax would be something like:
!Requires a psf and a coordinate set initially present
COORDINATE STATUS
COOR HBOND SELECTION "RESIDUE" END - SELECTION .NOT. "RESIDUE" END [VERBOSE]
If multiple structures are to be determined w. resp. to H-bonds then
FIRSTUNIT {unit number of first trajectory] NUNIT -[number of subsequent trajectories} -
BEGIN {frame to start with} NSKIP {number of time-steps that should be skipped} STOP {point where trajectory reading quits, i.e. the last frame for analysis} VERBOSE {gives a detailed report of the hydrogen bond pattern} - {other specifications}
See also the CHARMM documentation, "hbonds.doc" and "corman.doc" for further utilities.
Johan
