Thank you for your reply!
Now I know what's going on.
Best wishes
Yuan Min
> -----原始邮件-----
> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> 发送时间: 2017-12-05 06:12:11 (星期二)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file
>
> Hi Yuan,
>
> No worries. It is just a warning (if it is an error, MCPB.py will not finish the step). Not all of the metal ions (with various oxidation states) have VDW radii determined. Usually the cations of the same element have similar VDW radius, e.g. Fe2+ and Fe3+. Herein MCPB.py just tells it could not find the VDW radius for Os2+ and then it used the VDW radius of Os6+6 atom type (which is Os6+ ion) from UFF for the Os2+ ion the complex.
>
> Kind regards,
> Pengfei
>
> > On Dec 2, 2017, at 9:25 PM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
> >
> > Hi,
> >
> > I download the ZIP file from SI of MCPB.py reference.
> > http://pubs.acs.org/doi/suppl/10.1021/acs.jcim.5b00674
> >
> > cd work directory
> > type command "MCPB.py -i FAJYAR01.in -s 1"
> >
> > everything goes well,
> > until the last line of Building models in log:
> >
> > "Could not find VDW radius for element Os with charge +2, use the one of charge +6"
> >
> > By the way, there is a sentence in SI:
> >
> > The VDW radius of Os2+during the Merz-Kollman charge calculation was treated as 1.56Å and was obtained from the VDW parameters for “O6+6”atom typefrom the universal force field (UFF)
> >
> >
> > Need I do any modification to the input files?
> >
> >
> >
> >
> > Looking forward to receive your help.
> >
> >
> >
> >
> > Best wishes
> >
> > Yuan Min
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Dec 05 2017 - 04:00:03 PST
