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 - 19:00:04 PDT
