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

[Justin Lemkul]

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

-- 
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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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