Hi Zoran,
Sure, I'll keep it in mind.
Thanks again!:)
2016-07-05 14:37 GMT+08:00 zoran matovic <
zmatovic.kg.ac.rs>:
>
>
>
>
>
>
>
>
> Hi,
> Just don’t forget to source your .bashrc after u changed it:
> $source .bashrc
>
> That’s all
>
> Good luck
> Zoran
> Hi Zoran,
> Thanks for your kind advice. I'll try to install it.
>
> 2016-07-05 14:12 GMT+08:00 zoran matovic <zmatovic.kg.ac.rs>:
>
> Hi,
> Pengfei is giving u the best advices when MCPB.py is in question.
> However,
> in my opinion you should upgrade ambertools to ambertools16. There are so
> many reasons to do it. It is much improved and python packages and
> libraries
> are all (this time) in amber directory. You can leave old amber14 and
> install separately ambertools16 in /home/zhengyu/amber16/ dir. I think
> that
> MCPB.py has the updated version in ambertools16 and some important python
> pack. (nympy, scipy,..) are installed along with ambertools16.
> You may still use amber14 (if u have it) if u want to run pmemd.
>
> If u decide to install ambertools16 (suppose that u already have properly
> installed any valid mpi program) here is the Ross's suggestion for
> install:
>
> Change the path for AMBERHOME in your .bashrc file (say instead of
> AMBERHOME=/home/zhengyu/amber14 change to the right path for example
> AMBERHOME=/home/zhengyu/amber16). Place the tar ambertools16 file in
> your
> home dir.
>
> cd /home/zhengyu
> tar xvjf AmberTools16.tar.bz2
> cd $AMBERHOME
> ./update_amber --update
>
> ./configure gnu
> (say yes if it asks about python download)
> make -j8 install
> make clean
> ./configure -mpi gnu
> make -j8 install
> make clean
>
>
> Cheers
> Zoran
>
>
>
>
> -----Original Message-----
> From: Zhenyu Meng
> Sent: Tuesday, July 5, 2016 5:38 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MCPB.py cannot recognize Cl
>
> 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
> _______________________________________________
> 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
>
--
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 05 2016 - 00:00:03 PDT
