Re: [AMBER] Hybrid topology for mutating residue

From: David A Case <>
Date: Tue, 17 Sep 2019 08:43:11 -0400

On Mon, Sep 16, 2019, Aashish Bhatt wrote:
>I have followed the tutorial "*A Tutorial on Alchemical Free Energy
>Perturbation Calculations in NAMD" section 3 :**Mutation of tyrosine into
>trying to calculate free energy perturbation for mutating protein.
>I don't have idea how create hybrid topology file in amber.
>Can you please guide me idea for preparation of topology file.

You don't say whether or not you've read Chap. 21.1 ("Thermodynamic
integration") in the Reference Manual. Also, visit, click
on "Tutorials", then on "Thermodynamic integration using soft-core


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Received on Tue Sep 17 2019 - 06:00:03 PDT
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