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

gangotri dey holyriver6 at gmail.com
Fri Jul 21 14:59:57 CEST 2017


You might want to constrain the bond between the 2 protein chains.


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254

On Fri, Jul 21, 2017 at 8:56 AM, Sneha Vishwanath <
snehavishwanath09 at gmail.com> 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.
> Thanks in advance.
> Regards
> Sneha Vishwanath
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