Re: AMBER: Add hydrogen and charge calculation

From: Chris Moth <>
Date: Mon, 27 Aug 2007 15:33:25 -0500 (CDT)

I don't understand exactly what you are parameterizing - but you may find
this paper helpful:

J. Phys. Chem. B, 110 (26), 13166 -13176, 2006. 10.1021/jp060163v
Web Release Date: June 15, 2006

Copyright 2006 American Chemical Society
New-Generation Amber United-Atom Force Field

Lijiang Yang, Chun-hu Tan, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Piotr
Cieplak, James Caldwell, Peter A. Kollman,# and Ray Luo*

This united-atom forcefield is available in Amber 9. So, you can look in
the parameter files to see how residue data is assembled.

You might contact the authors to see if any automated scripts are
available to collapse the hydrogen charges onto the carbons.

One caveat: This forcefield currently lacks parameterization for
cross-linked cysteines.

> Dear Users,
> I am trying to add hydrogen in PDB file inside amber and then calculating
> the charges.
> But in next step i want to remove non-polar hydrogens by adding their
> charge
> onto the
> carbon atom. Is it possible to do such calculation inside amber? thank you
> in advance
> for your timely help.
> s

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Received on Wed Aug 29 2007 - 06:07:28 PDT
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