How to refine multiple poses from docking?

[Andrew Orry]

Q. How to refine multiple poses from docking.

A. 

If you are docking from the docking menu using project name 'MYPROJ' - your docked ligands will be in MyPROJ_answers.ob and the receptor will be called MYPROJ_rec.ob

To automate pose refinement one could use _scareRefine , originally it is meant as a stage in the SCARE protocol but it could be applied for just any poses from docking: 

 icm _scareRefine rec=MYPROJ_rec.ob lig=MYPROJ_answers1.ob lignum=<ligand index> 

 one can write a simple UNIX shell script that goes through ligand numbers (lignum=1, then lignum=2, lignum=3 etc ) and executes _scareRefine on them. This could be done with a loop or just repeated command lines. E.g. in bash

for inx in {1..10} 

do 

icm _scareRefine rec=MYPROJ_rec.ob lig=MYPROJ_answers1.ob lignum=$inx

 done