Hi Pengfei,
Thanks. My previous memory setting is 3000MB, now I change it to 6000MB.
Step 2 can work properly, with Zoran's help.
While for step 3, I met followed problem:
pymsmtexp.pymsmtError: The length of coordinates and ESP charges are
different!
Do you know where is the problem about this?
2016-07-09 23:50 GMT+08:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Zhenyu,
>
> The the intention of MCPB.py is making the *_opt.com <http://opt.com/>
> and *_fc.com <http://fc.com/> file use the same chk file, and in the end,
> after the *_fc.com <http://fc.com/> job finished, transfer the chk file
> to fchk file.
>
> It seems there is something wrong with the Gaussian calculations you
> performed which caused the chk file did not update correctly (due to it
> failed at the *_fc.com <http://fc.com/> calculation step).
>
> Here is a similar error other met:
> http://www.ccl.net/chemistry/resources/messages/2010/07/30.008-dir/ <
> http://www.ccl.net/chemistry/resources/messages/2010/07/30.008-dir/>.
>
> How much memory did you use in your calculation?
>
> Kind regards,
> Pengfei
>
> > On Jul 8, 2016, at 3:22 AM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
> >
> > 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 Mon Jul 11 2016 - 01:30:02 PDT
