Re: AMBER: How to assign /make the ionion bond?

From: <>
Date: Fri, 17 Oct 2008 19:06:26 -0400 (EDT)


> My understanding is that the FF only assign the covalent bond.
> How to assign /make the ionion bond?

two ions of opposite charges will feel a coulombic attraction without
setting any additional ff-parameters, so you dont need to set anything to
get this behaviour. However, the question if the energetics of ionic bonds
say in aqueous solution come out correctly in your simulation is a much
more tricky question and depends on picking the right ionic radii, water
models etc.

If you want to enforce a specific ion bond in your system that you know to
be present and dont find in the MD for some reason, you could always make
a pseudo-covalent bond between the ions via the xleap bond command (while
adding an appropriate frcmod file).

Regards and have a nice weekend,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Oct 19 2008 - 05:08:58 PDT
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