Re: About pbc

From: Jeff Comer (
Date: Tue Nov 15 2016 - 17:40:12 CST


You need to add -all to apply the wrapping to all frames.

For example:

pbc wrap -compound res -center origin -sel "noh" -all


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Tue, Nov 8, 2016 at 3:10 PM, Francesco Pietra <> wrote:
> Hallo:
> I used
> pbc wrap -sel "protein" -centersel "segname PRA" -center com -compond
> fragment
> followed by
> pbc wrap -sel all -centersel "protein" -center com -compound fragment
> for a long MD with a single chain protein having a Fe(II) active site
> (treated non bonded). I got all within the water box for the last frame and
> a few frames before that, not for all frames. I thought that the "all"
> should have forced all frames.
> Thanks for advice
> francesco pietra

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