# $Id: README,v 1.6.14.1 2007/03/25 21:32:28 oliver Exp $

BALL Utilities
==============

This directory contains some little utilities which are handy for everyday
use in molecular modeling:

add_hydrogens:

	Add missing hydrogens to PDB files and minimizes them while fixing all
	other atoms.

assign_typenames_from_rules:

	Assign typenames from rule files.

dcd2dcd:

	Converts CHARMm "enhanced" DCD trajectory files to simpler X-PLOR type
	DCD files. Use this program if some DCD reader does not know how to
	handle your (AMBER-generated) DCD file. It might help.

export_fragment:

	Reads a HyperChem or PDB file and creates a fragment database skeleton
	file with at least atom entries depending on the content of the input
	files.

pdb2amber_naming:

	Converts standard PDB files to PDB files which are conform to the AMBER
	naming scheme, i. e. usable for AMBER calculations. The resulting files
	will not necessarily be correct since there are some ambiguous cases
	which will not be resolved by this program. Instead a standard case will
	be assumed (like CYX for CYS residues which built a sulphur bridge).

pdb2dcd:

	Converts a bunch of PDB files to a dcd file containing the spatial
	information of these PDBs as trajectory information.
	
reconstruct_fragment:

  Reconstrucst degraded residues from fragment database information. If tou
	happen to have a PDB file which lacks some atoms, use this program to fix
	it.

rigid_docking:

	Run a rigid docking for two systems using the algorithm GeometricFit.
	There are two possible ways to store the docking results.
