Thanks for the initial feedback...I guess I'm still not clear on the steps
necessary to execute the simulation I want. By following the manual and
various online tutorials, I am able to successfully carry out antechamber on
a **single** copy of my molecule to generate charges, and can then minimize
the molecule, solvate it, and generate an MD simulation and movie...quite
straightforward and effective.
However, I now want to generate an appropriate set of files, coordinates,
charges, etc. that contain 2 (or more) copies of this same molecule, solvate
them, and carry out an MD simulation to see how/if they interact as a probe
of the first steps in self assembly. Is there a simple way to take the
optimized structure generated in amber for a single molecule and just clone
multiple copies of it for evaluation in an MD run? Xleap does not appear to
have a way to carry out a molecular copy step, or the ability to arrange an
array of molecules in various conformations. Sirius 1.2 allows me to import
a couple of molecules and position them independently, but does not seem to
be able to save the resulting molecular pair as a single file of coordinates
(maybe I haven't dug deeply enough into its operation??). The closest
analogies I've seen involve docking a substrate in an enzyme, but I have
been unable to translate those methodologies to the simpler molecules I'm
working with.
Again, thanks for any guidance,
Joe Bozell
University of Tennessee
------ Forwarded Message
From: Joe Bozell <jbozell.utk.edu>
Date: Wed, 22 Sep 2010 14:20:36 -0400
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: MD on an array of small molecules
I am attempting to use Amber for MD runs on a collection of small molecules
to observe their interaction during a self assembly process. I am able to
carry out MD runs on a single molecule in a water shell using antechamber
and subsequent steps. However, how does one carry out the same process on
multiple copies of a single molecule within a solvent box?
I have a pdb file for a pair of these molecules, and have used antechamber
to generate a prepi file. However, parmchk on the resulting file gives a
"segmentation fault" message, suggesting that the number of atoms may be too
large.
Is there a general method for carrying out this type of experiment within
Amber?
Thanks,
Joe Bozell
University of Tennessee
------ End of Forwarded Message
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Received on Thu Sep 23 2010 - 07:00:14 PDT
