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

From: Ashutosh Shandilya <>
Date: Wed, 6 May 2015 16:07:30 +0530

Try using "packmol" to make assembly (60) of DRUG molecules in pdb format.
Make sure after each DRUG there is TER to end the numbering of molecule.
Make frcmod and prepin file using antechamber. You can use waterbox using
tleap. You can now easily make topology and coordinate file using tleap and
run your simulation.

On 6 May 2015 at 15:09, 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??
> --
> Regards
> Tetala Srilaxmi
> M.S.(Pharm.)
> Dept. of Pharmacoinformatics
> NIPER, S.A.S. Nagar, Mohali
> _______________________________________________
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Received on Wed May 06 2015 - 04:00:02 PDT
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