HBPLUS

HBPLUS is a hydrogen bond calculation program The authors are I.K. McDonald, D. Naylor, D. Jones and J.M. Thornton. It will do the following:

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

The individual executables hbplus, accall, clean, chkqnh and chkqnh.scr should be in your default path (/sgi/local/bin/).

To use HBPLUS with all default parameters just type:

setup hbplus

and follow the prompts.

CONTENTS OF USERGUIDE

1 How to Use HBPLUS - Quick Instructions

2.1 Installation

2.2 Glossary of terms used in this guide, and in the program

2.3 The Command-Line Options

2.4 Input Files

2.5 Output File(s) Format

2.6 Adding New Residue Types

3.1 Introduction to Hydrogen Bonds

3.2 The Algorithm

3.2.1 Calculation of the Hydrogen Positions

3.3 Selecting Potential Hydrogen Bonds

3.4 Orienting ASN, GLN and HIS side-chains

4 References

Note: If you use results from HBPLUS in a publication please cite the following:

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