Re: [AMBER] how to center a polipeptide inside a solvent box

From: Jason Swails <jason.swails.gmail.com> Date: Thu, 1 Sep 2016 20:47:04 -0400

--
Jason M. Swails 
> On Sep 1, 2016, at 8:27 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> 
> Hi everybody,
> 
> I performed pH-REMD in explicit solvent, then I reconstructed the
> "trajectory" for each pH using cpptraj. Due to periodic boundary
> conditions, my polipeptide is not always centered in the snaphot (i.e. it
> looks like it is half outside the solvent box). I would like to know if it
> is possible to reorient the vectors and make my polipeptide be in the
> center of the solvent box, because I need the coordinates and charges for
> further QM calculations.
> 
> I hope I have been clear enough!
> Thanks,
> 
> Elisa
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