Your strategy seems to be correct. As I mentioned earlier, temp is not the
part of MM-PBSA. The effect of temperature is already there on the
conformational sampling, which you have written as traj. I am not sure
simulations at 2K temp diff is really distinguishable, as the fluctuation of
temp is usually more that 2K.
On Mon, Sep 20, 2010 at 9:44 PM, Khaled Barakat <kbarakat.ualberta.ca>wrote:
> Thanks for the reply.
>
> I have a protein-DNA complex that has been described in the literature
> to be sensitive to temperature changes. Experimentally, the complex
> can bind at temperature ranges (lower than 300K) and loses its binding
> with temperatures greater than 300K. So, I run MD simulations at
> different temperatures from T=293K to T315K in steps of 2K. that is 12
> MD simulations. for each simulation, I generated a trajectory. My idea
> then is to use these trajectories as inputs for mm-pbsa, one by one in
> order to analyze their binding energies. I was wondering if I need to
> specify the temperature for mm-pbsa as an input parameter, so it can
> use it in the energy conversion factors or any calculations that may
> require the knowledge of the temperature for each trajectory.
>
> I hope this clarify my procedure.
>
> Thanks,
> Khaled
>
> On 20-Sep-10, at 7:29 PM, manoj singh wrote:
>
> > Temperature affects the kinetic energy (velocity infact), and
> > kinetic energy
> > is not the part of MM-PBSA.
> >
> > What you want to do exactly?
> > --
> >
> > On Mon, Sep 20, 2010 at 8:39 PM, Khaled Barakat
> > <kbarakat.ualberta.ca>wrote:
> >
> >> Hello,
> >>
> >> I'm trying to run mm-pbsa at different temperatures to analyze the
> >> effects of temperature on the binding of a protein-DNA complex. I was
> >> wondering if there is a way to specify the running temperature as a
> >> parameter for the mm-pbsa script. I tried to set the temp variable to
> >> the desired temperature, but it seems there is no effect. I am using
> >> the mm-pbsa perl scripts with amber 10.
> >>
> >> Your help is so much appreciated.
> >>
> >> Thanks,
> >> Khaled
> >>
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Received on Mon Sep 20 2010 - 19:00:07 PDT
