AMBER Archive (2008)

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

From: Abhishek Singh (asingh7_at_ncsu.edu)
Date: Tue Jul 01 2008 - 14:02:28 CDT

Dear Dr Case , Dr Cheatham III
Your advise and support was really helpful and things are running great.
Thanks
Abhishek

On Mon, Jun 30, 2008 at 5:30 PM, Thomas Cheatham III <tec3_at_utah.edu> wrote:

>
> > 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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-- 
With Regards,

Abhishek Singh
Research Assistant
Material Science and Engineering
North Carolina State University
Raleigh, NC 27695-7907
Phone # 5179272418

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