Re: [AMBER] Obtaining necessary *.top for

From: Qinghua Liao <>
Date: Mon, 31 Dec 2018 16:12:16 +0100


You can either use tleap to generate the topology files or use parmed to
do that.

With tleap, you would need to run three times, for the complex, the
receptor and the ligand, respectively.
While with parmed, you would need to strip water and ions for the
complex, strip water, ions and the ligand for receptor,
and strip water, ions and the receptor for the ligand.

All the best,

On 12/31/18 3:08 PM, Sundar wrote:
> How to generate,, and files from
> an existing solvated_com.prm7 and solvated_com.mdcrd to be used for MM/PBSA
> calculation with ?

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Received on Mon Dec 31 2018 - 07:30:02 PST
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