Hi Fatima,
I can't remember if these are yet the default parameters, but they are
easily loaded with the following frcmods:
frcmod.ionsjc_tip3p
frcmod.ionsjc_tip4pew
frcmod.ionsjc_spce
depending, of course, on which water model you have loaded (default is of
course TIP3P).
Regards,
Brian
On Mon, Mar 5, 2012 at 12:18 PM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
>
> Dear Dr. Thomas E. Cheatham
>
> I came across your article and I wonder if this new parameterization for
> Alkali and Halide Monovalent Ion has been implemented in the latest version
> of Amber ..I am currently using Amber 11 and Amber tools 1.4
>
> I had issues with NaCl and KCL for concentration greater than 1 M and
> 0.5 M respectively. using TIP3P water model ..with Amber 9
>
> Now I wish to rerun the same system but with the improved parameterization
>
> many thanks
> Fatima
>
>
> Determination of Alkali and Halide Monovalent Ion Parameters for Use in
> Explicitly
> Solvated Biomolecular Simulations
> In Suk Joung† and Thomas E. Cheatham, III*,†,‡,§
> Department of Bioengineering, College of Engineering, and
> Departments of Medicinal Chemistry and of
> Pharmaceutics and Pharmaceutical Chemistry, College of
> Pharmacy, UniVersity of Utah, 2000 South 30 East,
> Skaggs Hall 201, Salt Lake City, UT 84112
> ReceiVed: January 8, 2008; ReVised Manuscript ReceiVed: April
> 30, 2008
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Mon Mar 05 2012 - 09:30:03 PST
