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 Sat Jan 23 2010 - 16:30:02 PST
