SECTION 1. HOW TO USE HBPLUS - QUICK INSTRUCTIONS
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hbplus.exe [options] [cleaned filename] [uncleaned filename]

HBPLUS inputs a Brookhaven Protein Database (Bernstein et al 1977) format
file, and outputs a list of potential hydrogen bonds.  

The interactions that qualify as hydrogen bonds must be between listed
donor and acceptor atoms, and have acceptable geometries.  A series of
command-line options can be used to change these criteria, output a
PDB-format file including generated hydrogen positions and extend the
hydrogen bonding atoms, amongst other possibilities.

The program is sensitive to relatively trivial mistakes in Brookhaven
files, and it is stronly recommended that you run a program to check and
correct the Brookhaven file before running HBPLUS.  Such a program,
"Clean", by DK Smith, R Laskowski and G Hutchinson, is distributed with
HBPLUS subject to the same conditions of use.

If HBPLUS is already installed, then to run it simply type . . .

example% hbplus /idata/new/p1mbd.new /data/pdb/p1mbd.pdb

The following output should be produced . . .

HBPLUS Hydrogen Bond Calculator v 2.25            Jan 22 14:54:13 GMT 1994
(c) I McDonald, D Naylor, D Jones and J Thornton 1993 All Rights Reserved.

Configured for 60000 atoms and 20000 residues.

Criteria

Minimum Angles; DHA 90.00, HAAA 90.00, DAAA 90.00
Maximum Distances; D-A 3.9, H-A 2.5, S-S 3.0
Maximum angles at aromatic acceptors DAAX 20.00, HAAAX 20.00
Minimum covalent separation 3 Covalent bonds

Processing "/idata/new/p1mbd.new"

Reading PDB file "/data/pdb/p1mbd.pdb" for CONECTs . . .
PDB file contained 50 CONECT records
1653 atoms selected from 541 residues.

50 CONRECS used.

Adding Polar Hydrogens.
NOTE: 1MBD/-0093-HIS NE2 forms 3 covalent bonds.
Checking for disulphide bridges . . .
0 disulphide bonds found.

Opened output file "p1mbd.hb2".
Checking for hydrogen bonds . . .
1244 hydrogen bonds found.
[end of output]

Your file of hydrogen bonds should be called p1mbd.hb2, and lie in the
current directory.  If HBPLUS is not already installed in your machine,
installion instructions can be found in section 2.1.