use positional (Cartesian) restraints. In Amber this uses ntr=1 and the
atom masks. You'll want to look at the manual for the mask syntax.
On Fri, Sep 28, 2012 at 8:54 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
>
> I want to generate the trajectory for a protein system. I want to relax
> first solvent and then protons followed by side chain of amino acids.
>
> Is SHAKE can do this? Or there is any other option.
>
> Please let me know
>
> Sindrila Dutta Banik
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Sep 28 2012 - 06:30:03 PDT
