[gmx-users] Long distance effects of mutation and stability

Jorge Fernández de Cossío Díaz j.cossio.diaz at gmail.com
Wed Apr 20 22:34:29 CEST 2016

I forgot to mention, I may also do simulations with the complex, mutated
protein + partner, again addressing the same questions. Will 100 ns be
enough, even for the larger complex?

In general, how can I know if the simulation time is enough, that I am not
missing modes of motion?

On Wed, Apr 20, 2016 at 4:32 PM, Jorge Fernández de Cossío Díaz <
j.cossio.diaz at gmail.com> wrote:

> I want to analyse the effects of a point mutation in a protein. The
> protein is 150 amino acids long.
> I have experimental evidence that a mutation has a distant effect in the
> protein. More precisely, the mutation affects the binding of the protein to
> another partner, even though the mutation occurs far from the binding site
> (almost on the opposite side).
> I don't know if the mutation is affecting the overall folded state, or if
> it has a long-range effect locally on the binding site.
> I have two broad questions:
> 1) Can GROMACS help me to answer this question? More precisely, are there
> papers published that use GROMACS to study stability effects of mutation,
> or long-range effects?
> 2) How long should I run the simulation to see long-range effects?
> Currently I have a 100ns simulation. In your experience, is this enough?

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