Sir
Actualy I am beginer for MD simulation and Amber I have already ran SGLD
for other protein for coformational search and I got the result.
In case of this protein I have ran the normal MD simulation for 10ns and as this
is a
large conformational change so I am not sure what MD simulation will be work.
I just want an idea.
> What is it that you want to learn that you do not already know? That will
> decide what type of simulation is best.
>
> On Jan 27, 2011 9:27 AM, "Sangita Kachhap" <sangita.imtech.res.in> wrote:
>
> Hello all
>
> I have a protein exist in two conformation inactive and active.To become
> active
> from inactive here is a N-terminus helix undergos ~90degree rotation.
>
> Is it possible to achive this by MD simulation?
>
> If possible then which technique should apply here?
>
> Since I ran very short 1.2ns SGLD and I didnt get any conformational
> changes.
>
> Should I increase the SGLD run?
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
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Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Jan 27 2011 - 08:30:05 PST
