On Mon, Sep 21, 2015 at 3:21 PM, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> Dear AMBER of the list,
>
> how to freeze atoms in an active site of a protein
> that do not have parameters and perform an MD ???
>
You still have to assign *some* parameters -- but if you do not care what
they are you can keep them set at 0 (which is the default value returned by
gaff whenever it cannot match a parameter).
You can then use the "ibelly" input variable to define flexible regions of
the system -- see the manual for more details.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 13:00:04 PDT
