AMBER Archive (2008)

Subject: Fwd: AMBER: prepare an initial structure in Amber

From: Lachele Foley (Lists) (
Date: Fri Aug 01 2008 - 09:52:50 CDT


I'm not certain I understand what you are asking. Let me know if I
got it wrong.

>From your images, I think you are changing molecular orientations
based on dipole, so that the dipoles oppose each other in an
alternating fashion. Is that right?

I don't know of any packages that will do that automatically for you.
Perhaps someone else knows of one. If you only have to do this once
for a few molecules in a system, it might be just as well to work out
the coordinates yourself and build a new coordinate file by hand.
Just make sure you get the proper number of coordinate entries and
that they are in the proper order. Since the topology and coordinate
files are independent of each other, you can generate the topology
file with the molecules in any arbitrary orientation and then change
the coordinates to be whatever you want. I suspect there are also a
number of packages that will let you visually manipulate the molecules
into approximate orientations. From there, you could save a pdb file
that leap can change into top and crd input files. But, if you want a
specific sort of alignment, that might require you to do a little

Does that sound like something close to an answer to your question?

:-) Lachele

---------- Forwarded message ----------
From: oguz gurbulak <>
Date: Thu, Jul 31, 2008 at 12:58 PM
Subject: AMBER: prepare an initial structure in Amber

Hi Dear Amber Developers,

Is it possible to prepare an initial structure in Amber like in the
figure I attached to the e-mail? In this initial structure the
molecules must be inversed neighbor by neighbor to provide zero dipole
moment. I'm waiting for your contributions.

Many thanks in advance

:-) Lachele
Lachele Foley

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to