AMBER Archive (2009)

Subject: RE: [AMBER] 8Mureabox

From: anna berteotti (annaberte_at_hotmail.com)
Date: Wed Mar 11 2009 - 03:45:03 CDT

Thank you for your suggestion!
So, if I have understood properly,
all the other parameter are taken from
the amber9/dat/leap/parm/ parameter
file, for example for the sigma used
to compute LJ interaction?
thanks again
anna

> Date: Tue, 10 Mar 2009 08:51:08 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] 8Mureabox
>
> 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
> LEaP.
>
> 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.
>
> ...good luck...dac
>
>
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