[gmx-users] Binding energy calculation

[Justin Lemkul]

On 9/13/15 9:21 AM, Malihe Hasanzadeh wrote:
> Thank you for your kind reply
> Which frame or which .pdb file is useful for starting calculation?

That's only something you can answer, because you know what you've done and you 
know what the reviewer is asking.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================