Scoreopt

Overview

Scoreopt allows you to rescore poses after a docking run is complete

Usage

Before using scoreopt, you should have a pdb (or eel1 or mol2) file with the poses to be rescored.

$mud/doscoreopt.csh  <filename.eel1> <path to grids>

Output is combine.rescores ( in the form of combine.scores )

<id> <shape> <elect> <VdW> <polar solv> <apolar solv> <total> <subdir>

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If you do not have an eel1 file and things are not running smoothly with your pdb file here are two options of how to get around it.

An eel1 file can be automatically created for you with this script:

 $mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions)

If you have special molecules the other was around it is to: a) read your pdb into chimera b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule) c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge') d) write out the molecule out as a filename.mol2 d) run the scoreopt script from above