Re: [AMBER] Docking before MD of scratch ligands OR not

From: Jason Swails <>
Date: Tue, 1 Dec 2015 08:13:12 -0500

On Tue, Dec 1, 2015 at 2:49 AM, muhammad tahir ayub <>

> Dear Amber Users
> I have performed 3D-QSAR studies on TRICYCLIC
> ANILINOPYRIMIDINES derivatives and designed 6 new inhibitors in the light
> of the newly designed model. I want to perform the Molecular Dynamics
> Simulation of the newly designed inhibitors thus is it necessary to dock
> the scratch ligands before the preparation from antechamber tool

‚ÄčNo. Antechamber is a tool you use on JUST the ligand. You need to
prepare a PDB file with just the single ligand residue, which antechamber
will then derive charges and atom types for. This is a separate step from

I suggest working through some of the tutorials that discuss antechamber at


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 01 2015 - 05:30:05 PST
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