AMBER Archive (2008)

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

From: steinbrt_at_rci.rutgers.edu
Date: Fri Oct 17 2008 - 18:06:26 CDT

Hi,

> 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,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu