HBONDMATRIX EXAMPLE INPUT
Chris Whittleston (csw34@cam.ac.uk) April 2012


This is input for a HBONDMATRIX GMIN run. The HBONDMATRIX keyword can be used to improve GMIN's efficiency when searching for and classifying ligand binding modes (poses) in protein binding pocket. 

At the moment, you must be using the AMBER potential to do this type of run. The example system used here is an influenza neuraminidase (NA) monomer, with the inhibitor oseltamivir (Tamiflu) bound. The files specific to the HBONDMATRIX keyword are the two named on the HBONDMATRIX line in the data file:

- hbond_residues.dat

This file contains a list of the residues (1 per line) which are involved in ligand binding, including the 
ligand (386). The hydrogen-bonds between these residues are used to determine the matrix that describes each 
binding mode.

- donors_acceptors.dat

This file contains (in AMBER ptraj format - see the AMBER Tools manual) the list of hydrogen-bond donor and 
acceptor atoms for the whole system. Much of this is the same for all natural proteins, but some varies with the ligand used. 

This input will perform 10 basin-hopping steps, changing only the conformation of the ligand using GROUPROTATION moves. We are also using the RIGIDINIT keyword to treat as many groups of atoms in the protein as possible as 
rigid bodies to speed up minimisation time.
