AMBER Archive (2009)

Subject: [AMBER] solutes in a simulation box

From: Workalemhu Berhanu (
Date: Sun May 31 2009 - 11:59:39 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?

Wu, C. et al have done it

J. Am. Chem. Soc., 2007, 129 (5), 1225-1232
---Eight simulations were performed on the GNNQQNY oligomer with CR
starting from two different configurations.--- The solute molecules were
immersed into a rectangle box of 7268 water molecules with dimensions of
either 58 × 101× 51 Å3 or 59 × 60 × 84 Å3.--- The periodic water box was
constructed in such a way that the solute was at least ~12 Å away from
the box surface and the minimum distance between the solute and the
image was ~24 Å. The effective concentrations of CR and the protofibril
oligomer were ~14 and ~7 mM, respectively—

Thank you

With best regards


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