[gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

Dear Justin

First I apologise for the error I had made in my previous mail. It's during
production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.


On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> > I followed the complex simulation tutorial. Minimisation for 2ns
> >
>
> FYI there is no time during energy minimization, so you did not do "2 ns"
> of
> minimization.
>
> > I used auto dock to dock ligand with protein. During simulation I find
> the
> > ligand out of protein. Is that usual?
> >
>
> This is probably a periodicity effect.  There's no way during the course of
> minimization that a ligand-protein complex can completely dissociate.  Use
> trjconv to make sure you've properly re-imaged the system.  A simple
> recentering
> should do it.
>
> -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*