Dear everyone,
I should correct the followiing sentence in previous e-mail:
>I am glad if anyone tell me the current E-mail address
>of professor Junmei Wang.
>
>But I am afraid that we should post a personal address to mailing >list.
I am glad if anyone tell me the current E-mail address
of professor Junmei Wang.
But I guess that we should not post a personal address to mailing list.
I am so sorry to confuse you.
-----Original message-----
From:Paul S. Nerenberg <psn.berkeley.edu>
To:kurisaki.fc.ritsumei.ac.jp,AMBER Mailing List <amber.ambermd.org>
Date:Tue, 27 Jul 2010 21:45:38 -0700
Subject:Re: [AMBER] Reference of ion parameters employed in parm99
You might want to try contacting Junmei directly about the Br-
parameters. There is some (old) contact info for Junmei posted on the
AMBER website (
http://ambermd.org/antechamber/antechamber.html), but
I'm guessing someone on the list has a more current e-mail address if
that one doesn't work.
Best,
Paul
On Jul 27, 2010, at 9:33 PM, kurisaki ikuo wrote:
> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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>
>
> $B7*:j0J5WCK(B
> $BN)L?4[Bg3X.8L?2J3XIt.8L?>pJs3X2J(B
> $B9b66BnLi8&5f<<=jB0(B $BGn;N8&5f0w(B
> $B")(B525-8577 $B<"2l8)ApDE;TLnO)El(B1-1-1
> E-mail: kurisaki.fc.ritsumei.ac.jp
>
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$B9b66BnLi8&5f<<=jB0(B $BGn;N8&5f0w(B
$B")(B525-8577 $B<"2l8)ApDE;TLnO)El(B1-1-1
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Received on Tue Jul 27 2010 - 22:30:04 PDT
