Re: [AMBER] organic molecule

From: Jason Swails <>
Date: Mon, 16 Mar 2015 10:15:59 -0400

On Mon, 2015-03-16 at 09:45 -0400, Lara rajam wrote:
> Dear Amber !
> If one want to perform a small molecule (organic molecule ) dynamics in
> water.
> Is it possible to do in AMBER.

Yes. It's basically the same as doing a regular protein with a bound
ligand in water. Generate the mol2 and frcmod files for the organic
molecule using antechamber.

Then load the molecule in tleap and solvate it using "solvateBox" or


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 16 2015 - 07:30:02 PDT
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