Hi Abhishek,
MCPB and MCPB.py are two different programs, the first one was written in C++ while the second one was newer and was written in python.
I suggest you to MCPB.py rather than MCPB in parameterizing the metal ion containing systems.
Based on your email it seems you used Amber14 or AmberTools15. I would suggest you to use AmberTools17 instead. Please see the first paragraph in this webpage: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Kind regards,
Pengfei
> On Jan 18, 2018, at 4:23 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> Hi I am trying to use MCPB to create the input file for Gaussian, but I am getting following error.
>
> Earlier I have worked on it but it was not a problem.
>
> Traceback (most recent call last):
> File "/nethome/axt651/apps/amber14/bin/MCPB.py", line 46, in <module>
> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py", line 7, in <module>
> from pymsmtmol.readpdb import get_atominfo_fpdb, writepdbatm
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/pymsmtmol/readpdb.py", line 5, in <module>
> from pymsmtmol.mol import Atom, Residue, Molecule
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/pymsmtmol/mol.py", line 2, in <module>
> from pymsmtmol.element import resnamel
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/pymsmtmol/element.py", line 4, in <module>
> from chemistry.periodic_table import AtomicNum
> ImportError: No module named chemistry.periodic_table
>
> MCPB.py -i NEP.in -s 1
>
> my inputfile is
> original_pdb NEP_H.pdb
> group_name NEP
> cut_off 2.8
> ion_ids 11049
> software_version g09
> ion_mol2files ZN.mol2
> naa_mol2files UNK.mol2
> frcmod_files UNK.frcmod
>
>
>
> But when I use MCPB
>
> MCPB -i NEP.in -s 1
>
>
> It gives me a MCPB.log file
>
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: readInputFile ###
> ### Message: Commands read:
> original_pdb NEP_H.pdb
> group_name NEP
> cut_off 2.8
> ion_ids 11049
> software_version g09
> ion_mol2files ZN.mol2
> naa_mol2files UNK.mol2
> frcmod_files UNK.frcmod
>
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ ###
> ### Function: elementParser ###
> ### Message: Reading XML with TINYXML
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: elementParser ###
> ### Message: Reading /nethome/axt651/apps/amber14/dat/mtkpp/elements.xml
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: original_pdb
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "original_pdb"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: group_name
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "group_name"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: cut_off
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "cut_off"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: ion_ids
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "ion_ids"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: software_version
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "software_version"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: ion_mol2files
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "ion_mol2files"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: naa_mol2files
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "naa_mol2files"
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: frcmod_files
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB ###
> ### Message: Unknown command: "frcmod_files"
> ### ### ### ###
>
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Received on Fri Jan 19 2018 - 11:30:01 PST
