Re: [AMBER] re-imaging bilayer

From: Dickson, Callum J <>
Date: Thu, 7 Jul 2016 15:43:37 +0000

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.



From: Daniel Roe <>
Sent: Thursday, July 7, 2016 10:37:57 AM
To: AMBER Mailing List
Subject: Re: [AMBER] re-imaging bilayer


On Thu, Jul 7, 2016 at 7:41 AM, Sally Pias <> 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?


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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