Hi Li.
Minimizations normally only look for the nearest local minima. If I
understood you correctly, you were hoping that in your case using
minimization your protein will have a conformational change of some chains
from lineal to curled. Maybe I'm mistaken, but for seeing that, you will
probably need to do some MD simulations.
The part of using the restraints is not very clear. I guess that you are
using some restraints to make the chains fold, rather than positional
restraints.
Have a nice day.
2015-10-14 11:17 GMT+02:00 Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>:
> Dear all,
>
>
> I have been running 3 times of minimization on my protein of interest with
> restraint being applied and hoping that the long chains present to curl
> back to the core protein.
>
> It is however, the energy has been reduced significantly but it seems like
> the long chains still look the same.
>
> Was wondering is this normal and many more minimization is required to
> have it curl back?
>
>
> Best regards,
>
> Li Zhe
>
>
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--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Wed Oct 14 2015 - 04:00:06 PDT
