Hi Dylan,
Good to know that. Small details count. : )
Good luck with your research!
Best wishes,
Pengfei
> On Jan 30, 2019, at 10:29 AM, Dylan Novack <tuj66686.temple.edu> wrote:
>
> Hi Pengfei,
>
> Thanks for getting back to me. I actually figured it out and went through
> the rest of the process without problems. There was a lowercase n in the ZN
> name in the mol2 file that I overlooked. Once that was corrected,
> everything worked great!
>
> Best Regards,
> Dylan
>
> On Fri, Jan 25, 2019 at 11:23 AM Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> wrote:
>
>> Hi Dylan,
>>
>> Yes, please send an email with your input files to my email address:
>> ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com> <mailto:ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>. I can
>> help to check.
>>
>> Pengfei
>>
>>> On Jan 22, 2019, at 7:53 PM, Dylan Novack <tuj66686.temple.edu> wrote:
>>>
>>> Hi Amber Users,
>>>
>>> I am trying to get ff parameters for a protein system I am working on
>> that
>>> coordinates 2 Zn ions. I'm using MCPB to do so and following the various
>>> tutorials online. The program can build the small model without error,
>> but
>>> when it comes to the standard model, the program gives me the error below
>>> for the second ZN;
>>>
>>> ***Creating the standard model...
>>>
>>> It contains the residue 285-CYS as normal.
>>>
>>> It contains the residue 354-HIP as normal.
>>>
>>> It contains the residue 358-GLU as normal.
>>>
>>> It contains the residue 468-CYS as normal.
>>>
>>> It contains the residue 499-CYS as normal.
>>>
>>> It contains the residue 501-HIE as normal.
>>>
>>> It contains the residue 525-ZN as normal.
>>>
>>> Traceback (most recent call last):
>>>
>>> File "/Users/tuj66686/bin/amber18/bin/MCPB.py", line 644, in <module>
>>>
>>> addred, lgchg, lgspin)
>>>
>>> File
>>>
>> "/Users/tuj66686/bin/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
>>> line 1899, in gene_model_files
>>>
>>> bdedatms, libdict, autoattyp)
>>>
>>> File
>>>
>> "/Users/tuj66686/bin/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
>>> line 1471, in build_standard_model
>>>
>>> attype = libdict[resname + '-' + atname][0]
>>>
>>> KeyError: 'ZN-ZN'
>>>
>>>
>>> I've checked that my atom types are correct in mol2 and pdb files and
>>> double checked my input file but can't determine what the problem is. Any
>>> help would be much appreciated. I can provide input files if need be.
>>> --
>>> Best Regards,
>>> Dylan Novack
>>> PhD Student
>>> Voelz Lab
>>> Temple University
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>
>
>
> --
> Best Regards,
> Dylan Novack
> PhD Student
> Voelz Lab
> Temple University
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> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Tue Feb 05 2019 - 09:30:02 PST
