Re: AMBER: loading pdb in leap to create parmeter files

From: David A. Case <>
Date: Sat, 5 Feb 2005 14:29:13 -0800

On Sat, Feb 05, 2005, wrote:
> I recieve an error message in the univeral editor
> stating that a number of atoms ( all atoms involved in heteroatoms specifically
> Guanosine triphosphate (GTP) and manganese ) stating, "FATAL: Atom .R,GTO
> 615>.A<pg 1> does not have a type."

You need to go to the "contributed parameters" data base (follow the link from
the Amber web site), and download input files and parameters for GTP. Look at
the tutorials to see how these would be used. You should expect to have to
fiddle with the LEaP input until everything "passes", but this procedure
should get you close.

If you have never used Amber before, I would suggest getting some experience
with protein simulations that lack co-factors and metals, before embarking on
a more complex task.

There are other ways to model GTP, but the procedure outlined above is pretty
good. You will have to look in the literature (e.g. to some of our work on
Ras/Raf, or lots of other papers) to get ideas for handling manganese or
magnesium. Modeling divalent ions is certainly an "advanced" topic in this

....good luck...dac

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Received on Sat Feb 05 2005 - 22:53:00 PST
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