Hi,
I'm trying to use MCPB.py on a complex with a ZN 4-coordinate metal center
(two Cys, one Hid, and one water), but am receiving the error as shown
below when the "MCPB.py -i xyz.in -s 1a" command is entered. I am using
Amber 14 with AmberTools 15 on a Linux workstation running RedHat 6.7 using
Python 2.7. We are not including a ligand in this process.
The xyz.in file looks like:
original_pdb xyz_fixed_H.pdb
group_name xyz
cut_off 2.8
ion_ids 3111
ion_mol2files ZN.mol2
naa_mol2files ZN.mol2 WAT.mol2
The error message is as follows:
Traceback (most recent call last):
File "/usr/local/amber/amber14/bin/MCPB.py", line 419, in <module>
watermodel, 2, sqmopt)
File
"/usr/local/amber/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 1167, in gene_model_files
ionids, chargedict, totchg, outf, watermodel, sqmopt)
File
"/usr/local/amber/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 984, in build_large_model
chg = str(int(chargedict[i]))
KeyError: 'H2'
I followed the tutorial, and have separated out the metal center as well as
the water, creating separate PDB files and mol2 files for each. Any
assistance would be appreciated.
Thanks,
Cooper
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Received on Sun Feb 21 2016 - 19:00:04 PST
