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
>alanine"*
>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 ambermd.org, click
on "Tutorials", then on "Thermodynamic integration using soft-core
potentials".
...dac
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Received on Tue Sep 17 2019 - 06:00:03 PDT
