Re: [AMBER] Lennard-Jones Parameters in prmtop

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Sun, 17 Jan 2010 17:27:41 -0600

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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Received on Sun Jan 17 2010 - 15:30:02 PST