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>
wrote:
> 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
> > _______________________________________________
> > 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
>
--
Best Regards,
Dylan Novack
PhD Student
Voelz Lab
Temple University
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Received on Wed Jan 30 2019 - 08:00:02 PST
