Re: [AMBER] re-imaging bilayer

From: Sally Pias <>
Date: Thu, 7 Jul 2016 07:41:17 -0600

I am following up on this old thread, as my group has had a lot of
difficulty imaging lipid bilayers consistently.

"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
regardless of what anchor is specified, because there is no single residue
that is always in the center of the bilayer. An easy fix might be to allow
a mask of two residues for the anchor (taking their center of mask as the
bilayer center). Then, one lipid tail from each bilayer leaflet could be
specified, allowing correct centering of the bilayer.

For most of our bilayer systems, "image" can be made to work well, using
various combinations of arguments for "center" and "image." However, for
some systems, the lipid tails are always placed on the sides of the image,
with all the water in the middle.

We have recently had a serious difficulty with this behavior of
"center/image" when following it with an electron density calculation using
"density." In several separate cases, the imaging was inconsistent over
time (300 ns; 300,000 frames), placing the lipids in the box center for
some frames and the water in the center for others. The "density" output
is, then, garbled, appearing to show a good deal of water in the center of
the bilayer and tails in the water. We do not get this behavior with
"autoimage." However, its uneven splitting of the water on the two sides of
the bilayer distorts the electron density curves and other analyses of
properties that vary according to bilayer depth (small solute free energy
by depth, in particular).

I would be happy to provide example input files and "bad" output examples,
if they would be helpful.

Thanks very much.

Sally Pias

From: Daniel Roe <
Date: Wed, 7 May 2014 08:45:45 -0600

Just to expand a bit on what Jason recommended, you want to choose as
your anchor molecule something which is close to everything you want
to remain "fixed". By default cpptraj chooses the first molecule as
the anchor, but in a bilayer this may not be the best choice. you
probably want to pick a molecule that is in the center of the bilayer
as your anchor. Remember also that many actions (like radial) do their
own imaging, so imaging prior to using such commands is not necessary.

Good luck,


On Wed, May 7, 2014 at 6:00 AM, Vijay Manickam Achari
<> wrote:
*> Dear sir, *
*> *
*> I have tried to re-image my bilayer (with water and lipids) after the
simulation about 300 ns. *
*> I use the command "autoimage" as prescribed in AmberTools and my earlier
posts. *
*> *
*> But my trials went no avail. *
*> *
*> I used commands like below, one after one in my trials in cpptraj: *
*> *
*> 1) autoimage *
*> *
*> 2) autoimage origin *
*> *
*> I also used ptraj: *
*> center * *
*> image center *
*> *
*> But all didnt work for me. I can see the bilayer shifts slowly in the
box and the water molecules in one layer shift to another layer. *
*> *
*> I need you help so much. *
*> *
*> You help is very precious. *
*> *
*> Thank you. *
*> *
*> Vijay Manickam. *
*> Chemistry Department, *
*> University of Malaya, *
*> Malaysia *
*> <> *
*> _______________________________________________ *
*> AMBER mailing list *
*> <> *
<> *

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 07 2016 - 07:00:03 PDT
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