It depends on how much you really want to restrain the ends. A restraint
force constant of 1 kcal/mol on all heavy atoms will keep residues fairly
rigid. At 10 kcal/mol, there will be virtually no movement. I would
suggest not using higher restraints than that (for dynamics).
HTH,
Jason
On Wed, Jul 4, 2012 at 3:21 AM, Rajendra Sharma <rajenbiotech.gmail.com>wrote:
> Dear All,
>
> I need to do some simulations on domain A of a protein where I have to
> constraint the ends(C and N terminal both). N terminal is attached to
> a membrane by a linker region while C terminal is attached to second domain
> of the same protein. Can some one suggest how much value of harmonic
> potential I should use to constraint the ends or some publications to read.
>
> Sincerely,
>
> Rajendras
>
>
>
> --
> Rajendra Sharma
> Junior Research Fellow,
> Computational Biophysics,
> *National Center for Biological Sciences,*
> (Tata institute of Fundamental Research)
> India.
> Mobile No. +91-9950675288
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 04 2012 - 09:30:02 PDT
