AMBER Archive (2008)

Subject: AMBER: big molecule numbers

From: Adrien Delmont (adriendelmont_at_yahoo.com)
Date: Thu Jul 24 2008 - 17:27:22 CDT

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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