AMBER Archive (2008)

Subject: RE: AMBER: big molecule numbers

From: Ross Walker (
Date: Fri Jul 25 2008 - 03:10:05 CDT

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.




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,




From: [] On Behalf Of
Adrien Delmont
Sent: Thursday, July 24, 2008 3:27 PM
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,



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