AMBER Archive (2009)

Subject: [AMBER] create a simulation box

From: Workalemhu Berhanu (
Date: Sat May 30 2009 - 22:06:24 CDT

Dear users of amber
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


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