Re: [AMBER] re-imaging bilayer

From: Sally Pias <sallypias.gmail.com>
Date: Tue, 19 Jul 2016 20:49:20 -0600

Following up on this thread...

Thanks to Dan, Callum, and Amy for your helpful suggestions.

Doing the following in cpptraj seems to have resolved our issues:

autoimage
center ":PA"
image ":WAT"

Best regards,
Sally

--
Sally Pias
Assistant Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
(575) 835-6204
www.nmt.edu/~spias
spias.nmt.edu
On Thu, Jul 7, 2016 at 8:37 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Jul 7, 2016 at 7:41 AM, Sally Pias <sallypias.gmail.com> wrote:
> >
> > "Autoimage" does a great job but splits the water unevenly on the two
> sides
> > of the bilayer, leaving a very thin water layer on one side. It does so
>
> What if after you 'autoimage', you then re-center the bilayer (with
> 'center') and then 'image' *only* the water?
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Jul 19 2016 - 20:00:03 PDT