Hi Pengfei,
I'm now trying to install Ambertools16. Meanwhile I try to run gaussian
using the existing .com file.
But when I ran XXX_small_fc.com, I met a problem. The program can terminate
normally, while when I use formchk to extract Force constant, no
information can be obtained.
pymsmtexp.pymsmtError: There is no 'Cartesian Force Constants' found in the
fchk file. Please check whether the Gaussian jobs are finished normally,
and whether you are using the correct fchk file.
I checked the XXX_small_fc.log file, and found there's a message:
End of G2Drv Frequency-dependent properties file 721 does not exist
I don't know whether it's related to the problem.
Do you have any idea about this?
2016-07-06 9:21 GMT+08:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Zhenyu,
>
> This error seems because of your permission setting. At this time, as
> Zoran suggested, installing the AmberTools16 could be a better way.
>
> Kind regards,
> Pengfei
>
> > On Jul 4, 2016, at 11:38 PM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> >
> > 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
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Received on Fri Jul 08 2016 - 00:30:03 PDT
