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

[Sneha Vishwanath]

@ 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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