[gmx-users] Protein and Ligand position restraint

[Amir Zeb]

Thank you Justin,
Got it

Amir

On Sun, Feb 26, 2017 at 7:52 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/24/17 1:19 AM, Amir Zeb wrote:
>
>> Hello gmx users,
>>
>> I want to conduct md simulation to explore the comparative stability and
>> interaction mechanism of the reference compound (experimentally
>> determined)
>> and the newly screened candidate molecules by virtual screening approach.
>> The gromacs version 5.0.7 is installed on my cluster. I want to listen to
>> your suggestions regarding:
>>
>> 1. Is it rational to restraint the position of the protein and/or ligand?
>> 2. If position restraint is necessary, which part of the system should I
>> restraint?
>> 3. Also, at which steps, I may restraint them, means NVT, NPT and md
>> production? Because the Justin tutorial mentioned the release of restraint
>> immediately after equilibration steps.
>>
>> I have co-factor FAD as the essential part of the protein, so I would like
>> to consider protein-FAD as single moiety. I searched from gmx-user archive
>> and Justin Tutorial, but I could not get a sound proof for this dilemma.
>>
>> Hope to listen to you soon
>>
>>
> The purpose of position restraints is to allow the solvent to relax around
> the solute(s) of interest without perturbing them due to the initial
> artificiality in the system.  In this regard, it is sensible to restrain
> the protein and whatever bound ligand(s) may be present during
> equilibration.  Restraints during production make no sense.  Flexibility
> and dynamics are the point of running an MD simulation :)
>
> -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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