[gmx-users] Topology parameters for ligand

[Justin Lemkul]

On 1/7/17 10:29 PM, tasneem kausar wrote:
> Thank you for your reply
>
> In last section of your tutorial you have suggested some changes to made in
> mdp file. That can be used for solvation free energies.
> For free energy calculation of protein drug complex, is it only lambda
> restraint to be defined?
>

Along with a complex system of [intermolecular_interactions] that preserve the 
relative orientation of the ligand.  This is a very complex calculation in 
practice.  See examples on alchemistry.org and in the literature in works by 
Roux, Im, Karplus, etc.  My tutorial is not very useful for such calculations; 
it is extremely basic relative to what is needed to carry out a binding free 
energy calculation.  I only mentioned it there because so many people asked 
about it and I wanted to clear up any confusion.

-Justin

> On 8 Jan 2017 01:45, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/7/17 6:05 AM, tasneem kausar wrote:
>>
>>> Dear all
>>>
>>> I am following Justin's tutorial methane in water for free energy
>>> calculation. I am using Gromacs-5.1.4. The charges of methane in topology
>>> are set to zero. So following the same protocol, is it relevant to set the
>>> charges at zero in topology of the drug. I am confused because in tutorial
>>> of Sander (ethanol in water) charges are present in the topology file.
>>>
>>> Please tell me the difference in both the tutorials and how can I apply it
>>> to drug that I want to study.
>>>
>>>
>> The charges in my tutorial are set to zero because the stated goal of that
>> tutorial is to reproduce *only the LJ portion of the hydration free energy*
>> to match a published paper.  This creates a very simple, robust system.  If
>> you want to calculate a real, meaningful hydration or binding free energy,
>> charge transformation is required.
>>
>> -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

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