[gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*