Hi Zhenyu,
> On Jul 11, 2016, at 4:16 AM, Zhenyu Meng <fdmm1989.gmail.com> wrote:
>
> 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:
>
Good to know that.
> pymsmtexp.pymsmtError: The length of coordinates and ESP charges are
> different!
>
Can you send the Gaussian log file of the large model to my email address: ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>? I can help to do a check.
Kind regards,
Pengfei
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jul 11 2016 - 12:30:02 PDT
