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 Sat Dec 29 2018 - 14:30:03 PST
