AMBER Archive (2008)

Subject: Re: AMBER: Regarding force field ff02 and ion library

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Mon Jun 30 2008 - 16:30:05 CDT

> On Mon, Jun 30, 2008, Abhishek Singh wrote:
> >
> > > loadamberparams frcmod.ionsjc_tip3p
> >
> > Could not open file frcmod.ionsjc_tip3p: not found
>
> The "ionsjc" parameters were not in Amber9, only began starting with Amber10.
>
> But you can still use them, since you can download the amber10 parameters
> here:
>
> http://ambermd.org/amber10.ffparms.tar.bz2

Also, please note that those ion parameters are non-polarizable and tuned
for specific water models (i.e. hence the water model in the name, i.e.
ionsjc_tip3p, ionsjc_spce, ...); they will likely not be transferrable to
a polarizable water model (without some re-fitting) and may not be
balanced with a polarizable RNA model...

  [Note that the paper describing the new monovalent ion
   parameters should be in JPCB ASAP very soon now.]

--tec3

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