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#455 10/25/03 09:12 PM
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cao Offline OP
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Dear all,
I want to count the hbond number of a residue, how can I do it?
Thanks in advance!


cao #456 10/26/03 08:29 AM
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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


cao #457 10/26/03 03:25 PM
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..and there's also a script (Scripts Archive/hbonds.inp) which has been authored by Professor Lennart Nilsson...


Moderated by  lennart, rmv 

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