Hi Adrien,
This really depends on how you want your initial 'box' of molecules to be
aligned etc. The simplest option is just to solvate your molecule with a
large number of the same molecule.
e.g.
foo = loadpdb foo.pdb
foobox = copy foo
solvatebox foo foobox 12.0
And this will give you a 'solvent' box containing lots of your own
molecules. You can then do:
solvatebox foo TIP3PBOX 8.0
if you want some water as well. Note though that this will likely need a LOT
of equilibration to correctly mix your system.
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Adrien Delmont
Sent: Thursday, July 24, 2008 3:27 PM
To: amber.scripps.edu
Subject: AMBER: big molecule numbers
Dear AMBER developers,
I?m studying on an example MD simulation about a small formamide molecule .
I?m using my own force field parameters since my molecule is not described
enough with the GAFF. Apart from simulation of small formamide molecule
in Amber , my goal is to increase molecule numbers and run MD simulation
with big molecule numbers like 500 or 1000 in Amber . And I thought that I
should use Antechamber tool but I?m not sure about that . So I want to
get more information about this matter.
How can I use big molecule numbers for the simulation ? Could you give me
the information about the basics of this procedure?
Thanks for your help!
Best regards,
Adrien
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Received on Sun Jul 27 2008 - 06:07:43 PDT
