Re: [AMBER] create a simulation box

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Tue, 2 Jun 2009 16:08:46 +0100

http://www.ime.unicamp.br/~martinez/packmol/

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
<wberhanu.mail.ucf.edu> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 03 2009 - 01:09:57 PDT
Custom Search