RE: AMBER: params for cofactors

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 29 Aug 2005 13:10:55 -0700

Dear Michael,

> I'd like to assemble a collection of cofactors having AMBER atom types
> and charges. Has anyone done a rigorous qm calculation for any of the
> following?:
>
> cAMP, cGMP, porphin, ADP, GDP, ATP<GTP, protophorphyrinIX, heme, NAD,
> NADP, FAD, FADhH, others? Where might parameter sets to use?

Take a look at this website that is referenced from the amber website.

http://pharmacy.man.ac.uk/amber/

It contains a range of different parameter sets included most of those you
mention above along with references to the papers they were published in.

You should also check the $AMBERHOME/dat/contrib directory of an Amber 8
installation.

All the best
Ross

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Received on Mon Aug 29 2005 - 21:53:04 PDT
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