Thanks Dac
My interest is turn off VDW potential for selected regions in order to let
atoms pass through each other.
On Thu, May 8, 2014 at 12:32 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, May 08, 2014, Asaminew Haile wrote:
>
> > I've an RNA molecule, with one single strand region and I would like do
> > pulling by adding restraints. To do so, I need to turn on SOFTCORE
> > potential. I'm aware of that in the amber manual, softcore potential is
> > under the thermodynamic integration. I was wondering if someone has any
> > idea how to use the softcore other than TI.
>
> Amber's "softcore" may not be what you think it is. Ours only works in the
> context of TI. (If I'm forgetting something, others on the list can chime
> in.)
>
> ...dac
>
>
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--
Asaminew H. Aytenfisu, Grad Student
David Mathews' group
Department of Biochemistry and Biophysics
University of Rochester Medical Center
Office: 3-8807
601 Elmwood Avenue, Box 712
Rochester, NY 14642
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Received on Thu May 08 2014 - 10:00:06 PDT
