AMBER Archive (2008)

Subject: AMBER: Problems for use manganese molecules

From: vallespardojl_at_chem.leidenuniv.nl
Date: Fri Nov 21 2008 - 03:06:37 CST

Hi everybody!

I'm new with the AMBER.
I think that my problem is similar to Lili's problem. I have installed
AMBER8 in my Linux machine, and I've followed the tutorials and seems
that all works ok. But, in my research I'm working with a Mn cluster.
First of all I become the .xyz file with the coordinates of my
molecule into a .pdb file with Openbabel. But when I use the
antechamber in order to create the .prepin file, and then solvate the
molecule appears a error message because the program doesn't recognize
the metallic atoms.
I think that I need put in the database file all the parameters of the
new atom type, but how can I do it?

Thanks for the help!

José Luis

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