See below.
On Sep 23, 2010, at 8:46 AM, Bozell, Joseph John wrote:
> 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
There are ways of getting LEaP to do what you want, I believe, but the packmol
program (
http://www.ime.unicamp.br/~martinez/packmol/) was created to do
exactly what you want. Look at the example of a mixed urea-water box, IIRC.
Of course you will need the concentration you want to simulate -> the number of
molecules of your solute in the simulation cell. Plus the number of waters to
achieve a density of ~1.0. My experience is that simulation cells created with
packmol drop precipitously in energy in the first few steps of dynamics due to
reorientation of the molecules leading to a lower electrostatic term, so
an initial short dynamics run at 100K is a good (but not strictly necessary)
idea. Then proceed on with the regular equilibration of temperature, density,
etc.
Since simulation systems set up with packmol start out containing solvent, if
you need a vacuum prmtop (e.g., for postprocessing analysis), you will have to
strip the solvent, then generate the prmtop on the stripped PDB. Kind of
backwards to the ordinary way of doing things.
Hope this helps,
Bud Dodson
> ------ 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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--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Thu Sep 23 2010 - 07:30:09 PDT
