Dear Fatima,
I use 0.15M KCl in my work... I look at intracellular enzymes. I used the 08
ion parameters simply to be current, not because I needed them because of
precipitation problems at very high concentrations of salt with the default
ion parameter set.
Good luck,
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: fatima chami <fatima.chami.durham.ac.uk>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Sat, 23 Jan 2010 18:27:41 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Lennard-Jones Parameters in prmtop
>
>
> 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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>>>
>>>
>>>
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Received on Sun Jan 24 2010 - 11:30:03 PST
