Distinguished Sir or Madam
I'm trying to use MCPB.py for performing parameterizations for both the metalloprotein and organometallic compound systems. I followed the steps to prepare the PDB and mol2 files for the non-standard residues and metal ions in the tutorial and there was errors in the first step of generating the PDB, Gaussian and fingerprint modeling files.
Here are my error messages:
*****************************************************************
* *
*=======================Metal Site Information===================*
* *
******************************************************************
***Selected Metal ion NI is atom 37834 in residue 2476-NI1
146-GLN.OE1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
2475-F31.NA is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
2475-F31.NB is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
2475-F31.NC is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
2475-F31.ND is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
***The following residues are in the Metal Site:
Residue 146-GLN
Residue 2475-F31
Residue 2476-NI1
***The small model contains the following residues:
[146, 2475, 2476]
***The large model contains the following residues:
[145, 146, 147, 2475, 2476]
******************************************************************
* *
*=======================Building models==========================*
* *
******************************************************************
***Creating the small model...
It contains the residue 146-GLN as sidechain coordinated.
It contains the residue 2475-F31 as normal.
It contains the residue 2476-NI1 as normal.
Totally there are 125 atoms in the small model.
Traceback (most recent call last):
File "/usr/local/theochem/amber16/amber16/bin/MCPB.py", line 644, in <module>
addred, lgchg, lgspin)
File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1895, in gene_model_files
smspin, addred, outf, sqmopt)
File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1380, in build_small_model
AtNum = Atnum[gatm.element]
KeyError: '2'
This problem confused me. I tried to rebuild the model and repeat the preparations in the tutorials. It seems to be that the number of electrons in the model is wrong. But I don't know how to solve it.
Could someone help me out of the problem? Any response will be highly appreciated!
Yours,
Wu Jue
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Received on Wed Mar 04 2020 - 20:00:02 PST
