[gmx-users] Protein ligand complex simulation

[Mark Abraham]

Hi,

Look at your docking result before you use it for something else. (Same
goes for any computed result from any software.)

Mark

On Mon, 3 Apr 2017 14:06 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> The ligand is out of protein in the very first frame of production run.
>  Then that should be my docking error.?
>
> On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > > 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.
> > >
> >
> > Then watch the recentered trajectory to see what happened.  Dissociation
> > should
> > be apparent, and smooth if the PBC effects have been correctly accounted
> > for.
> > If the dissociation is real, either the initial position was unfavorable
> > (docking is sometimes incorrect!) or the topology of the ligand was
> > inadequate
> > and thus you got a poor model of the interactions.
> >
> > -Justin
> >
> > >
> > > 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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> >
> > --
> > ==================================================
> >
> > 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*
> --
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