AMBER Archive (2005)

Subject: AMBER: Working with a nickel-organometallic compound

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue May 31 2005 - 18:36:30 CDT

I'm trying to model a nickel containing organometallic compound. The
nickel needs to be bound to the organic portion of the molecule in a
similar layout to a crown ether. I've generated the molecule without
the nickel and run it through antechamber to assign atom/bond types,
etc. I created custom atom types for the nitrogen atoms that will bind
to the nickel and then used prmchk to create a frcmod file and then
manually edit it.

My problem is with getting information on the nickel. I was going to
load the organic portion, then a nickel in the correct position in
xLeap, make the nitrogen nickel bonds, CHECK the unit and supply the
new needed lengths, angles, etc with a separate frcmod file that I'll
create. Has anyone worked with Nickel in Amber and would you be
willing to share your information?

Thanks a lot,

Kara Di Giorgio

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