On Mon, Feb 25, 2013 at 6:32 AM, Anne Kichler <a_kichler.ymail.com> wrote:
> Hello Everyone,
> I'm new member.
>
> How can I create a pseudo-atom?
AMBER has no notion of a pseudo-atom. In fact, I would argue that
`pseudo-atom' is not well-defined. What is it? What properties does it
have? The answer will naturally depend on what the person defining the
pseudo-atom wants to do with it.
Your only option, really, is to use a real atom and adjust its properties
(e.g., charge, lennard-jones parameters, etc.) to suit your needs (starting
with a monoatomic ion seems like a natural choice). This is an advanced
technique that will require careful thought and preparation, as well as a
superficial understanding of how sander/pmemd uses data in a topology file
to calculate the potential.
ParmEd can help modify the topology file if you decide to go this route,
but I would definitely suggest trying to re-design your experiment to avoid
having to use this construct in the first place.
Moreover, is there a pseudo-atom library?
>
No, for the reasons stated above.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 25 2013 - 05:00:06 PST
