AMBER Scoring in DOCK

Warning this is out of date and will be updated - SRB June 3, 2005.

Design

The Amber_Score class methods are modeled after those in class ZAPscore.
The public interface methods override the virtual methods of class Base_Score.
The underlying implementation is based on NAB.
The private methods contain NAB program fragments.

Installation

Obtain NAB version 4.5.3 (plus bug fixes)
http://www.scripps.edu/case/
Create the config.h for NAB.
Execute dock/src/nab/mirror.
Build DOCK.

Temporary Limitations

Amber_Score can only handle one unique receptor and one ligand during the
course of one DOCK run.  The user must input filenames for a combined
receptor ligand pdb and AMBER prmtop; the ligand must be positioned at the
tail of these files.

Only the linux makefile has been modified to use Amber_Score.


Input Options

amber_score_verbose
Control for Amber-side verbosity.
"yes" produces a detailed energy breakdown for every scoring attempt.
The default is "no" - minimal output.

amber_score_minimization
Control for Amber-side minimization.
"everything" requests a minimization of both the receptor and the ligand.
"ligand" requests a minimization of only the ligand.
"nothing" requests no minimization; this is the default.

