Another option you could try is:
center mass origin :1-384
image center origin familiar
Where you should alter the :1-384 mask so that it covers all of the lipid residues in your bilayer.
Best,
Callum
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Thursday, July 7, 2016 10:37:57 AM
To: AMBER Mailing List
Subject: Re: [AMBER] re-imaging bilayer
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 Thu Jul 07 2016 - 09:00:04 PDT
