[gmx-users] protein -ligand complex dissociating during simulation

[RAHUL SURESH]

It sounds like some internal dihedral problem. Request you, check on it.

On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath <
snehavishwanath09 at gmail.com> wrote:

> @ Justin: I have re-imaged  the trajectory with trjconv using and still the
> ligand dissociates from one of the chain but remain bound with the other
> chain.
>
> @ Gangotri: I am not sure how constraining the bond between protein might
> help. Can you please elaborate if possible.
>
> Thanks in advance.
>
> Sneha
>
> On Fri, Jul 21, 2017 at 6:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/21/17 8:56 AM, Sneha Vishwanath wrote:
> >
> >> Dear all
> >>
> >> I am simulating a dimeric protein, with each subunit bound to a small
> >> molecule. During the simulation, one of the ligands is dissociating from
> >> the chain and moving all around the chain while the same ligand remains
> >> bound to the chain during simulation. Experiments show that the ligand
> >> binds to both the subunit which is further supported by the experimental
> >> structure of the protein-ligand complex (which I have used for the
> >> simulation). The simulation is for 50 ns and it usually starts
> >> dissociating
> >> after 10 ns.
> >>
> >> Any thoughts on why could it be happening and how it can be
> circumvented?
> >> Any help would be useful.
> >>
> >>
> > Are you sure this is not simply a PBC artifact?  Have you
> > re-imaged/centered the trajectory appropriately with trjconv?
> >
> > -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*