Hi Dylan,
Yes, please send an email with your input files to my email address: 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
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Received on Fri Jan 25 2019 - 08:30:03 PST
