Hi Pengfei,
It seems working.
But when I run test, some errors occurs:
mkdir -p /home/zhengyu/amber14/amber14/AmberTools/test/pymsmt/mcpb/g03 ; \
cp /home/zhengyu/amber14/amber14/AmberTools/src/pymsmt/tests/g03/*
/home/zhengyu/amber14/amber14/AmberTools/test/pymsmt/mcpb/g03/ ; \
cd /home/zhengyu/amber14/amber14/AmberTools/test/pymsmt/mcpb/g03 ;
./Run.pymsmt
/bin/sh: line 2: ./Run.pymsmt: Permission denied
make: *** [test] Error 126
2016-07-05 11:17 GMT+08:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Zhenyu,
>
> Yeah. I would suggested you to use the version 2.0c:
> https://github.com/Amber-MD/pymsmt/releases/tag/v2.0c <
> https://github.com/Amber-MD/pymsmt/releases/tag/v2.0c>.
>
> Please let me know whether it works.
>
> Kind regards,
> Pengfei
>
>
> > On Jul 4, 2016, at 11:14 PM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> >
> > Hi Pengfei,
> > What I used is the original version in Ambertools15. I installed it maybe
> > last year.
> > In your opinion, a newer version can overcome such problem?
> > Thanks again!
> >
> > 2016-07-05 11:07 GMT+08:00 Pengfei Li <ambermailpengfei.gmail.com>:
> >
> >> Hi Zhenyu,
> >>
> >> Which version of MCPB.py did you use? Did you use the newest version?
> >>
> >> Kind regards,
> >> Pengfei
> >>
> >>> On Jul 4, 2016, at 11:00 PM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> >>>
> >>> Dear Amber Users,
> >>> Recently I'm using MCPB.py to build a Pt-complex(no bio molecule).
> >>> My complex has one chloride ion connected to Pt, but when using MCPB.py
> >> to
> >>> proceed it, the Cl cannot be recognized within metal pocket.
> >>>
> >>> ***Selected Metal ion PT is atom 1 in residue 1-PT
> >>> 2-RES.N1 is in 2.8 Angstrom of 2-RES.N1
> >>> 2-RES.N2 is in 2.8 Angstrom of 2-RES.N2
> >>> 2-RES.N3 is in 2.8 Angstrom of 2-RES.N3
> >>> ***The following residues are in the Metal Site:
> >>> Residue 1-PT
> >>> Residue 2-RES
> >>> ***The large model contains the following residues:
> >>> [1, 2]
> >>>
> >>> I'm not quite sure whether it will affect the later processing, is
> there
> >>> anyone able to help?
> >>> Your help will be high appreciated!
> >>>
> >>> --
> >>> Sincerely,
> >>> Mr. Meng Zhenyu
> >>> Division of Chemistry and Biological Chemistry
> >>> School of Physical and Mathematical Sciences
> >>> Nanyang Technological University
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Sincerely,
> > Mr. Meng Zhenyu
> > Division of Chemistry and Biological Chemistry
> > School of Physical and Mathematical Sciences
> > Nanyang Technological University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Mon Jul 04 2016 - 21:00:03 PDT
