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
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>> 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 Tue Jul 05 2016 - 18:30:03 PDT
