Hi Zoran,
Thanks for the help!
When I ran small_fc.com, I have such chk command:
%Chk=pt1p1_small_opt.chk
I think this will use the .chk file from small_opt job and then write to
the same file, so as you said, this procedure formatted the .chk file,
right?
I will try to add fcheck to my input.
2016-07-08 16:16 GMT+08:00 zoran matovic <zmatovic.kg.ac.rs>:
> Hi,
> You probably formatted the first opt checkpoint file so u created file with
> no freq infos. Good idea is to add "fcheck" keyword to the small_fc.com
> file
> and after gaussian finish the job rename the "test.fchk" into appropriate
> name: smal_opt.fchk. Now the things should be OK to continue MCPB.py.
>
> Cheers
> Zoran
>
> -----Original Message-----
> From: Zhenyu Meng
> Sent: Friday, July 8, 2016 9:22 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MCPB.py cannot recognize Cl
>
> 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
> _______________________________________________
> 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 - 02:00:02 PDT
