AMBER Archive (2009)

Subject: [AMBER] help with parameters for ions

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Tue Jun 02 2009 - 07:46:14 CDT

Hello,
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

where they give new parameters for Rmin and epsilon, and I am trying to
introduce these values in the amber force field using the instructions
given in http://ambermd.org/Questions/vdw.html

I have one doubt about the procedure. When I load the frcmod*.in, I am not
deffining the charge anywhere, do I have to load also some file of the type
of prepin, or something like that? In the link it is not explained how you
define the new ions to be recognized by the command "addions" in amber. I
have tried to write to Todd J. Minehardt, as in indicated, but I receive
the mails back.

Please, could anyone give me some advice?

Thank you very much for your help in advance,
Best wishes, 

-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona
rebeca_at_mmb.pcb.ub.es

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber