[Dock-fans] Docking to Molecular Dynamics

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 30 11:43:32 PDT 2009


Hi,

On Tue, Jun 23, 2009 at 05:27:32PM -0700, Eric Pettersen wrote:

> > I am trying to find out what methods are used to prepare docking
> > complexes for molecular dynamics. Currently I am using autodock4 and
> > trying to prep the docking complexes for gromacs using amber03 force
> > fields. My ligand has some incompatibilities. I hear that UCSF has a
> > good workflow to bring results to molecular dynamics easier.

> Maybe you mean Dock Prep? Dock Prep documentation is here: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/dockprep/dockprep.html
> 

In addition, DOCK's Amber score runs Amber MD via NAB:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm

Scott



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