AMBER Archive (2009)

Subject: Re: [AMBER] help with parameters for ions

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jun 02 2009 - 08:46:40 CDT

On Tue, Jun 02, 2009, rebeca wrote:
>
> I am doing simulations using a KCl concentration 1M and I have problems of
> crystallization of ions in the simulations. I have seen in the literature
> that this is normal with Amber parameters for ions.
>
> I have found a paper
> "Determination of Alkali and Monovalent Ion Parameters for Use in
> Explicitly Solvated Biomolecular Simulations"
> S Joung, Thomas E Cheatham, J. Phys. Chem. B, Vol. 112, No. 30. (1 July
> 2008), pp. 9020-9041.
> http://www.citeulike.org/user/softsimu/article/3863549

Frcmod files for these parameters are in the frcmod_ionsjc_* files in
$AMBERHOME/dat/leap/parm. You can use those directly, and also see how the
frcmod files were created, in case you want to use your own or other
parameters.

...hope this helps...dac

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