[Dock-fans] Prepare Amber

Scott Brozell sbrozell at rci.rutgers.edu
Mon Jun 15 12:09:43 PDT 2009


Hi,

On Mon, Jun 15, 2009 at 12:05:07PM -0400, Rahul Banerjee wrote:
> 
> I am trying to rescreen a set of ligand and rank them according to the Amber score. I am using prepare_amber.pl script (provided with Dock6). I found this program to be extremely slow (even slower than my dock6 run). Is it really the case or I am doing some thing wrong? Can I use multiple processors to run prepare_amber.pl ?
> 

Is it slow during this step:
Generating AM1-BCC charges.  This may be time consuming.
?
We have a new version with:
An option to use the ligand charges from the DOCK_ranked_mol2_file
automates efficient rescoring with multiple scores.
that can eliminate that step, but note that Amber Score is more sensitive
to charges than other Dock Scores; so the existing charges in the 
DOCK_ranked_mol2_file should be good ones.

> Also is there any limit on the number of ligands prepare_amber.pl can handle?

No.

Scott



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