Re: [AMBER] Obtaining necessary *.top for

From: Elvis Martis <>
Date: Tue, 1 Jan 2019 05:05:54 +0000


Alternatively, you could use "" to get the necessary files.

Best Regards

Elvis A F Martis

Molecular Simulations Group,

Department of Pharmaceutical Chemistry,

Bombay College of Pharmacy,

Kalina, Santacruz [E],

Mumbai 400098,


Institute Web-address:<>

Research Group Web-address:<>

Personal Web-address:

From: Qinghua Liao <>
Sent: 31 December 2018 20:42
Subject: Re: [AMBER] Obtaining necessary *.top for


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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