ADL: Ligand size limit for Autodock 4 and moving to MD

Shultz, Jack JShultz at
Tue Feb 26 05:12:05 PST 2008


I would like to know how well you combine the results from Autodock with
Amber. I'm looking at potentially modeling enzyme catalyzed reactions by
docking MD snapshots interpolated from CI-NEB method using
Semi-Empirical Field. 


-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at]
On Behalf Of Francesco Pietra
Sent: Monday, February 25, 2008 5:00 AM
To: autodock
Subject: ADL: Ligand size limit for Autodock 4 and moving to MD

Independently from the reliability of the results, which is the limit to
(organic) ligand size to a multimer protein?

With "organic" I mean a molecule without repeating units, typically a
product, flexible, made of 120 to 500 atoms.

Does Autodock 4 accept mol2 files, such as prepared by Antechamber
(Amber), or
is it restricted to united atom?

At any event, how to use the docking results with Autodock 4 to carry
molecular dynamics? (ideally with Amber).


francesco pietra (new to the list)

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