Hi Fati,
I did succeed to use the newly optimized parameters for ions for
concentration up to 1M with AMBER9.
Follow the instructions by Dean and I believe you can do it.
Jianhui
On Sat, Jan 23, 2010 at 7:27 PM, fatima chami <fatima.chami.durham.ac.uk>wrote:
>
> Hi,
>
> I am just wondering whether you have managed to use the newly optimized
> parameters for ions to model higher concentration of salt > 0.2M
>
> I would have to do it the same way as your while using Amber 9
>
> Many thanks
> Fati
>
> On 18/01/2010 01:53, "Jianhui Tian" <jianhuitian.gmail.com> wrote:
>
> > 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 Tue Jan 26 2010 - 12:30:02 PST
