AMBER Archive (2009)
Subject: Re: [AMBER] 8Mureabox
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Mar 10 2009 - 07:51:08 CDT
On Mon, Mar 09, 2009, anna berteotti wrote:
> I'm trying to use the 8Mureabox.off in order to
> simulate protein-urea interaction.
> I can't understand which are the parameters
> used for urea molecules from the 8Mureabox.off 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 8Mureabox.off
file. You could use these to create a mol2 format file and read that into
Alternatively, you could probably load the 8Mureabox.off file into xleap,
then use the unit editor to erase everything but one urea molecule, and
save that as a new unit.
AMBER mailing list