Hi Hunter,
Good to know that! Happy New Year!
Best,
Pengfei
> On Dec 29, 2018, at 5:17 PM, Hunter Wilson <wils1872.umn.edu> wrote:
>
> Afternoon Pengfei,
>
> Changing the atom type did the trick! After restarting from the first step,
> and using the electronic structure calculations, I was able to get the
> force constants in step 2.
>
> Thanks again,
> Hunter
>
> On Fri, Dec 21, 2018 at 5:22 PM Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> Hi Hunter,
>>
>> This is because you don’t have the mass parameter for atom type “CL”.
>>
>> Change the atom type of CL in CL.mol2 to “Cl” (AMBER ff14SB has parameters
>> for the atom type “Cl") and start over from the first step, then the
>> problem will be solved.
>>
>> Hope it helps,
>> Pengfei
>>
>>> On Dec 16, 2018, at 3:48 PM, Hunter Wilson <wils1872.umn.edu> wrote:
>>>
>>> Good afternoon,
>>>
>>> I've run into a hiccup using the MCPB.py program, and I can't figure out
>>> how to proceed. I'm using it in order to develop some force constants
>> for a
>>> non-heme iron system. I've successfully completed step 1, and I have all
>>> the necessary .log files from my Gaussian calculations. The next part
>> where
>>> I use step two in order to develop my .frcmod files seems to be where I'm
>>> having issues.
>>>
>>> When I run this command: MCPB.py -i 2fct_mcpb.in -s 2
>>>
>>> I get the following error:
>>> Traceback (most recent call last):
>>> File "/home/ambikab/wils1872/software/anaconda3/bin/MCPB.py", line 582,
>>> in <module>
>>> ff_choice, gaff, frcmodfs, watermodel)
>>> File
>>>
>> "/home/ambikab/wils1872/software/anaconda3/lib/python3.7/site-packages/mcpb/gene_pre_frcmod_file.py",
>>> line 132, in gene_pre_frcmod_file
>>> print('YES', atyp2 + massparms[atyp1], file=fmf)
>>> KeyError: 'CL'
>>>
>>> Based on this, it seems like it's having trouble finding my chloride
>> .mol2
>>> file, so it's probably a naming issue. I have tried to keep my naming
>>> consistent across my various input files.
>>>
>>> Attached are all of the inputs necessary for the calculation. Any
>>> assistance would be greatly appreciated!
>>>
>>> Best,
>>> Hunter
>>>
>>> --
>>> Hunter Wilson
>>> Chemistry PhD Student
>>> General Chemistry Teaching Assistant
>>> wils1872.umn.edu
>>>
>>> Department of Chemistry
>>> University of Minnesota- Twin Cities
>>> <CL.mol2><2fct_from_server_total_fixed.pdb><2fct_mcpb.in
>>> <FE.mol2><O2M.mol2><SUC.mol2>_______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>>
>
>
> --
> Hunter Wilson
> Chemistry PhD Student
> General Chemistry Teaching Assistant
> wils1872.umn.edu
>
> Department of Chemistry
> University of Minnesota- Twin Cities
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Received on Thu Jan 10 2019 - 08:00:04 PST
