Hi Ning,
If you follow that tutorial exactly as it is (using a very old version of AMBER, probably AMBER7), the parameters used are those of Åqvist.
J. Phys. Chem., 1990, 94 (21), pp 8021–8024
If you look at:
http://ambermd.org/tutorials/advanced/tutorial8/files/wt1mg_dry.parm7 <
http://ambermd.org/tutorials/advanced/tutorial8/files/wt1mg_dry.parm7>
You’ll find exactly.
%FLAG LENNARD_JONES_ACOEF
2.25261100E+02
%FLAG LENNARD_JONES_BCOEF
2.83930348E+01
Which are the parameters disclosed in the 1990 paper.
You should check your own topology file (parm7) to make sure you know exactly which LJ parameters were used.
Cheers,
Mauricio.
+++++++++++++++++++++++++++++++++++++++++++++++
Mauricio Esguerra Neira, Ph.D.
Researcher
Department of Cell and Molecular Biology
Uppsala University
Phone Number: (+46)073-678-5334
mesguerra.org <
http://mesguerra.org/>
mauricio.esguerra.icm.uu.se <mailto:
mauricio.esguerra.icm.uu.se>
https://orcid.org/0000-0002-1775-586X <
https://orcid.org/0000-0002-1775-586X>
+++++++++++++++++++++++++++++++++++++++++++++++
> On Jan 3, 2019, at 9:19 PM, Zuo, Zhicheng <Zhicheng.Zuo.unthsc.edu> wrote:
>
> Hi Ning:
>
> In preparing your force field file with leap, the default Mg2+ ion parameter set points to the "normal usage set" by Li, Merz, et al for the current AMBER version,
>
> if you do not explicitly specify. You may refer to Table 1 in our recent paper for a summary of commonly used Mg2+ models.
>
> https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00627
>
>
>
> All the best,
>
> Zhicheng
>
> ________________________________
> From: ? ? <knsherry.hotmail.com>
> Sent: Thursday, January 3, 2019 10:01:15 AM
> To: amber.ambermd.org
> Subject: [AMBER] Literature about magnesium ion parameters in tutorial A8
>
> Dear all,
>
> I used the magnesium ion parameter in Amber tutorial A8 (https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial8%2Fdownload.htm&data=02%7C01%7CZhicheng.Zuo%40unthsc.edu%7C8aac581ed0ef4fe5a26f08d671a58cae%7C70de199207c6480fa318a1afcba03983%7C0%7C1%7C636821353175970108&sdata=6iQoKM%2Bsy%2FJG9l%2FB%2BgHkeZoz3FZ0Nbt1Fd%2BUhrDubOc%3D&reserved=0) in my work. And I want to cite the source of this parameter or any literatures used this parameter as reference.
> After searching, I did not find appropriate literature (some used other magnesium parameters, the others did not introduce clearly). Could anyone tell me any literatures used this parameter?
>
> Thanks a lot!
>
> Best wishes,
> Ning
> Shanghai jiaotong University
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Received on Fri Jan 04 2019 - 03:30:02 PST
