AMBER Archive (2009)

Subject: Re: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Sep 10 2009 - 21:04:53 CDT

On Thu, Sep 10, 2009, Workalemahu Berhanu wrote:

> Is it possible to do periodic boundary condition using implicit
> solvent simulation with amber?

No.
> I also would like to learn how to do
> restrain on some inter atomic distance say the central atom of the ligand
> and the reside of the peptide which is close to the ligand.

Treat this as an "NMR" restraint.

...good luck...dac

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