Dear Dr. Cuebas,
Thanks for this reply. I will take a look at Cheatham's JPCB 2008 paper.
What can I do if I dont have amber10? Is there a way to get ions08.lib and
frcmod.ionsjb_XXXXXX? Are they compatible with amber9?
Still I wonder how the Lennard-Jones-Acoef and Lennard-Jones-Bcoef are
calculated. Many thanks for clarification.
Jianhui
On Sun, Jan 17, 2010 at 6:27 PM, Dean Cuebas
<deancuebas.missouristate.edu>wrote:
> Why don't you use just use the more complete and current parameters from
> Cheatham's group (2008) that already comes with amber10?
>
> in leap:
>
> loadoff ions08.lib
> loadamberparams frcmod.ionsjc_XXXXXX
>
> where you choose the below water model you desire.
>
> frcmod.ionsjc_spce
> frcmod.ionsjc_tip3p
> frcmod.ionsjc_tip4pew
>
> Cheers,
>
> Dean
> --
> Dr. Dean Cuebas, Associate Prof of Chemistry
> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
>
>
> > From: Jianhui Tian <jianhuitian.gmail.com>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > Date: Sun, 17 Jan 2010 11:07:42 -0600
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] Lennard-Jones Parameters in prmtop
> >
> > Hi all,
> >
> > I am now trying to do simulations with ions parameters from Chen et al
> (J.
> > Phys. Chem. B 2007, 111, 11884-11887) and ffamber99sb together. After
> > generate the prmtop file, I need to identify the Lennard-Jones parameters
> > for NaCl and change them accordingly. I have read the prmtop format and
> > identify the IAC, ICO for NaCl, then I found CN1 and CN2 for NaNa, NaCl,
> > ClCl parameters. But I am confused how the CN1 and CN2 are calculated.
> The
> > following is what I used:
> >
> > Lennard-Jones interaction:
> > A/(r^12)-B/(r^6)
> >
> > where A is LENNARD_JONES_ACOEF in prmtop file, and B is
> LENNARD_JONES_BCOEF
> > in prmtop file.
> > Then (A/B)^(1/6) should give sigma(NaCl), and
> > sigma(NaCl)=(R(Na)+R(Cl))/(2^(1/6)).
> >
> > Sigma(NaCl) I got from A,B of prmtop and from R(Na), R(Cl) of parm
> doesn't
> > agree with each other. I am really confused how CN1 and CN2 are
> calculated.
> > Could you please give me a hint if you know how these parameters are
> > calculated? Thanks a lot.
> >
> > Jianhui
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Sun Jan 17 2010 - 18:00:02 PST
