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 Thu Jan 18 2018 - 14:30:02 PST
