HBPLUS v 3.03 - Hydrogen Bond Calculator

Ian McDonald mcdonald at bsm.bioc.ucl.ac.uk
Thu Aug 11 07:30:26 EST 1994

HBPLUS v 3.03

Hydrogen Bond Calculation Program


HBPLUS is a hydrogen bond calculation program that has been developed
in-house over the course of over four years and has been used in
countries as diverse as the USA, Taiwan and South Africa. It . . 

 o Calculates the Geometries of all Hydrogen Bonds 
 o Optionally Lists of Neighbour Interactions 
 o Calculates Hydrogen Positions 
 o Deals with Hydrogens that can Occupy More Than one Position 
 o Optionaly includes amino-aromatic H-bonds. 
 o Supports Full Customisation, eg of 
    o H-bond criteria
    o Donor and Acceptor Atoms types
 o Analyses H-bonding Near Asn, Gln and His Side-Chains and Suggests
   Optimal Conformation 
 o Supports .hbplusrc Files 
 o Outputs PDB File Including Extrapolated Polar Hydrogen Positions 

Technical Side

It is written in ANSI C and has been checked on several UNIX systems
as well as VAX/VMS. It unfortunately requires too much memory to run
on an IBM PC or an Apple Macintosh.

If you would like a copy of HBPLUS, simply download the 
confidentiality agreement, sign it, snailmail it to me and I'll email
you a password that you can use to un-crypt the ftp-able
hbplus.tar.Z.cr file, after loading it to disk as a binary file. The
agreement essentially promises not to give anyone outside your lab
copies of HBPLUS, and to reference us if you use HBPLUS results in a
paper - HBPLUS is free to academic users. HBPLUS compiles using a

This release also includes ACCESS to determine accessible surface
areas, and CLEAN to tidy Brookhaven files. These programs are written
by other people and also covered by the confidentiality agreement. 

ftp: bsm.bioc.ucl.ac.uk ( /pub/hbplus
WWW: <http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/>


HBPLUS is (c) I.K. McDonald, D. Naylor, D. Jones and J.M. Thornton
ACCESS is (c) S. Hubbard 1992-4
CLEAN is (c) D.K. Smith, R. Laskowski and G. Hutchinson 1992-4


I.K. McDonald and J.M. Thornton (1994), "Satisfying Hydrogen Bonding
Potential in Proteins", JMB 238:777-793. 

mcdonald at bsm.bioc.ucl.ac.uk

Confidentiality Agreement

Correspondence to:
Ian McDonald (PG)
Biological Structure and Modelling Unit
Department of Biochemistry and Molecular Biology
University College London
Gower Street

Email mcdonald at uk.ac.ucl.bsm

                    HBPLUS - Hydrogen Bond Calculation


In regard to the HBPLUS program, specified in Appendix 1 herewith (the
Software) supplied to us, the copyright and other intellectual property
rights to which belong to the authors, we


undertake to the authors that we shall be bound by the following terms and

1. We will receive the Software and any related documentation in confidence
and will not use the same except for the purpose of the department's own 
research. The Software will be used only by such of our officers or
employees to whom it must reasonably be communicated to enable us to
undertake our research and who agree to be bound by the same confidence.
The department shall procure and enforce such agreement from its staff for
the benefit of the authors.

2. The publication of research using the Software must reference "McDonald
IK & Thornton JM (1994), 'Satisfying Hydrogen Bonding Potential in
Proteins', Journal of Molecular Biology 238:777-793"

3. Research shall take place solely at the department's premises at


4. All forms of the Software will be kept in a reasonably secure place to
prevent unauthorised access.

5. Each copy of the Software or, if not practicable then, any package
associated therewith shall be suitably marked (and such marking maintained)
with the following copyright notice: "Copyright 1991-3 Ian McDonald, Dorica
Naylor, David Jones, S Hubbard, R A Laskowski and Janet M Thornton All
Rights Reserved".

6. The Software may be modified but any changes made shall be made
available to the authors.

7. The Software shall be used exclusively for academic teaching and
research. The Software will not be used for any commercial research or
research associated with an industrial company.

8. The confidentiality obligation in paragraph one shall not apply:

   (i)  to information and data known to the department at the time of
	receipt hereunder (as evidenced by its written records);

  (ii)	to information and data which was at the time of receipt in the 
	public domain or thereafter becomes so through no wrongful act of
	the department;

 (iii)	to information and data which the department receives from a third
	party not in breach of any obligation of confidentiality owed to
	the authors.

Please sign this Undertaking and return a copy of it to indicate that you 
have read, understood and accepted the above terms.

		      For and on behalf of _____________________________


		      Dated ............................................

                      Address __________________________________________

		      Country _________________ Postcode ______________
                      Telephone ________________________________________

                      Electronic Mail Address to which HBPLUS shall be

                      sent _____________________________________________



Files to be included

         1. hbplus.h              }
         2. hbp_gen.c             } Source program files,
         3. hbp_inpdb.c           } ,formerly hbplus.c
         4. hbp_findh.c           }
         5. hbp_hhb.c             }
         6. hbp_main.c            }
         7. hbplus.man         } Documentation
	 8. accall.f              } Supplemental, (c) S. Hubbard
	 9. vdw.radii	          } "ACCESS" / "NACCESS"
	10. clean.f	       } Supplemental, (c) DK Smith et al.
	11. brkcln.par         } "BRKCLN"
	12. chkqnh		  } C Shell Script
	13. Makefile	       } Unix Makefile

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