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
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Received on Mon Jul 04 2016 - 23:30:01 PDT
