Dear Prof. Nerenberg,
Thank you for your kind message.
It's really helpfull.
Yes, I cannnot access Iodide parameters.
I am so sorry to confuse you.
I recognize that nobody know the reference of Br- parameters
in parm99.
Is my acknowledgement correct?
Yours sincerely,
Ikuo Kurisaki
PS.
Thank you for information about JC paramters.
I recognize that they are very useful.
We now perform systematic examination of ionic solution.
Conventional ion models were also examined as well as new ones.
-----Original message-----
From:Paul S. Nerenberg <psn.berkeley.edu>
To:AMBER Mailing List <amber.ambermd.org>,kurisaki.fc.ritsumei.ac.jp
Date:Tue, 27 Jul 2010 21:04:12 -0700
Subject:Re: [AMBER] Reference of ion parameters employed in parm99
Hi Ikuo,
Your message is a bit confusing because you say that you both can and
can't access references for I (iodide). Assuming that you can't
access the one for I, it is the AMBER ff86 reference: http://dx.doi.org/10.1002/jcc.540070216
. If you meant to say that you can't find the Cl (chloride)
reference, that one is here: http://dx.doi.org/10.1021/jp9717655.
Best,
Paul
P.S. If it's not too late in your simulation process, you might want
want to try out the Joung and Cheatham parameters for the halides
(developed circa 2008). These seem to behave much better than the old
parameters, which were taken from many different sources (as you've
seen). If you have AMBER 10 or 11, these are located in $AMBERHOME/
dat/leap/parm/frcmod.ionsjc_tip3p, ../frcmod.ionsjc_tip4pew, and ../
frcmod.ionsjc_spce.
On Jul 27, 2010, at 8:21 PM, kurisaki ikuo wrote:
> Dear Amber developers,
>
> We need to know references of LJ potential parameters
> of halide ion employed in parm99.
>
> However, we cannot find the enough information anywhere.
> Of course, we know that parm99.dat file have following information:
>
> F 1.75 0.061 Gough et al. JCC 13,(1992),
> 963.
> Cl 1.948 0.265 Fox, JPCB,102,8070,
> (98),flex.mdl CHCl3
> Br 2.22 0.320 Junmei(?)
> I 2.35 0.40 JCC,7,(1986),230;
>
> We can access the references of F and I.
> However, we cannot access the references of Br and I.
>
> To our knowledge, this is only information we can use.
> Even in Amber mannual, there are no information for
> these halide parameters.
>
> We are most grateful if you would tell us it.
>
> Thank you for your kind support.
>
> Sincerely yours,
>
> Ikuo Kurisaki
>
>
> $B7*:j0J5WCK(B
> $BN)L?4[Bg3X.8L?2J3XIt.8L?>pJs3X2J(B
> $B9b66BnLi8&5f<<=jB0(B $BGn;N8&5f0w(B
> $B")(B525-8577 $B<"2l8)ApDE;TLnO)El(B1-1-1
> E-mail: kurisaki.fc.ritsumei.ac.jp
>
> _______________________________________________
> AMBER mailing list
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$BN)L?4[Bg3X.8L?2J3XIt.8L?>pJs3X2J(B
$B9b66BnLi8&5f<<=jB0(B $BGn;N8&5f0w(B
$B")(B525-8577 $B<"2l8)ApDE;TLnO)El(B1-1-1
E-mail: kurisaki.fc.ritsumei.ac.jp
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Received on Tue Jul 27 2010 - 22:00:03 PDT
