On Mon, Sep 21, 2015 at 3:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> 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).
>
gah...
returned by parmchk2*, not gaff.
> 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
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 13:00:05 PDT
