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
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Received on Sat Jul 09 2016 - 09:00:02 PDT
