[gmx-users] Topology parameters for ligand

[tasneem kausar]

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?

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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