Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER

From: Jason Swails <>
Date: Wed, 06 May 2015 09:15:07 -0400

On Wed, 2015-05-06 at 15:09 +0530, srilaxmi reddy wrote:
> How to simulate bulk molecules in AMBER.. i mean i got the mol2 file of a
> DRUG molecule. now i have to simulate 60 molecules of it.. how to do it??

The mol2 file simply provides the residue template library. If you
generate a PDB file that contains 60 residues of the small molecule
defined in the mol2 file, then leap will know to transfer the parameters
and topology from the mol2 file to each copy in your PDB file.

The problem is then reduced to "how do I create a PDB file with 60
copies of a single molecule". You can try some commands in leap (like
"copy" and "solvateBox" -- not sure if that one will work without a box
unit), but you might have better luck with other programs (packmol comes
to mind).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed May 06 2015 - 06:30:04 PDT
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