AMBER Archive (2009)

Subject: Re: [AMBER] 8Mureabox

From: David A. Case (
Date: Tue Mar 10 2009 - 07:51:08 CDT

On Mon, Mar 09, 2009, anna berteotti wrote:
> I'm trying to use the in order to
> simulate protein-urea interaction.
> I can't understand which are the parameters
> used for urea molecules from the file.
> I was wondering if there's a possibility to extract
> from it a sort of prepin file for just one urea molecule,
> or if there's somewhere a file with the topology and
> parameter for one urea molecule.

You will need to do a little hand-editing. The charges and atom types for
a urea molecule are in the first eight atom records of the
file. You could use these to create a mol2 format file and read that into

Alternatively, you could probably load the file into xleap,
then use the unit editor to erase everything but one urea molecule, and
save that as a new unit.

...good luck...dac

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