Dear developers and users
I am trying to model a metalloprotein-ligand complex using the MCPB.py tool
of AmberTools17. My protein contains two zinc atoms. I used to prepare a
single PDB (and MOL2) file that combines both zinc atoms when I was using
AmberTools16. But with the newer version I had to separate them into two
files so that Antechamber can prepare the mol2 files. However, when I
reached the first step in MCPB.py modeling I had problems. First of all, I
could not prepare any of the metal centre models and the error message was
related to ZN1. I changed ZN to the corresponding atom name (ZN1 or ZN2) in
the mol2 files. After this adjustment, the PDB file of the small model was
generated. However, those for the standard and large models as well as the
fingerprint files and GAMESS input files were not generated. I had this
error message:
File "/apps/amber17/bin/MCPB.py", line 644, in <module>
addred, lgchg, lgspin)
File
"/apps/amber17/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
line 1895, in gene_model_files
smspin, addred, outf, sqmopt)
File
"/apps/amber17/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
line 1380, in build_small_model
AtNum = Atnum[gatm.element]
KeyError: 'Z'
Can you please help me to resolve this issue.
Any advice will be greatly appreciated.
Best regards
Amani Eshtiwi
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Received on Thu Sep 21 2017 - 10:00:02 PDT
