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 Tue Jan 22 2019 - 17:00:03 PST
