[gmx-users] Binding energy calculation

[Malihe Hasanzadeh]

Thank you for your kind reply
Which frame or which .pdb file is useful for starting calculation?
On 13 Sep 2015 17:40, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote:
>
>> Hi
>>
>> I have simulated a protein-ligand with gromacs and submitted it. My
>> reviewer asked me about calculation of binding energy. Which tutorial is
>> acceptable and suitable for me to do it?
>>
>
> Either free energy calculations (alchemical transformation) or PMF.  Note
> that you will need to use the new [intermolecular_interactions] in version
> 5.1 to use the free energy code and get a meaningful free energy of binding.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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