Re: [AMBER] running a MD with a innert gas

From: case <>
Date: Sat, 11 Jun 2011 13:58:37 -0400

On Fri, Jun 10, 2011, Adrian Roitberg wrote:

> look at the manual and tutorials on how to make an frcmod file.
> > I want to run an MD of one atom of argon in a box of water, but I've
> > come up up with a problem Amber does not has parametrized the Argon,
> > so I cannot make amber recognize the atom to generate the topology
> > file, I have the Lennard-Jones parameter, but how can I add this new
> > atom to the amber library?

Just a note that you also need to create a library (or prep) file that will
describe the "residue" that contains the argon atom. It's easiest to start
from one of the ions (say in $AMBERHOME/dat/leap/lib/solvents/cmd) and
copy some existing single atom residue, renaming it to argon.

...good luck...dac

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Received on Sat Jun 11 2011 - 11:00:03 PDT
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