AMBER Archive (2009)

Subject: Re: [AMBER] create a simulation box

From: Gustavo Seabra (
Date: Tue Jun 02 2009 - 10:08:46 CDT

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q: Why do mountain climbers rope themselves together?
A: To prevent the sensible ones from going home.

On Sat, May 30, 2009 at 11:06 PM, Workalemhu Berhanu
<> wrote:
> Dear users of amber
> Hi
> I am novice to the amber software package. I have an x-ray structure of a hexa- peptide and I  prepared the  structure of the organic molecule ( I have used GAFF and created the topology and coordinate files for my organic molecule) whose interaction with the peptide I want to study with amber Molecular Dynamic Simulation using an implicit  solvent.. I want to create a simulation box by introducing three monodispersed replicas of the same hexapeptide, with or without the presence of single small organic molecules.  I also want to set the concentration ratio peptide: compound of 3:1 and 1:1. Would you please give me a guide on how this could be done?
> Thank you
> With best regards
> Workalemahu
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