Dear Amber developers,
I'm new to amber22 thus requesting your help with the following error.
After trying the basic tutorial I'm learning to use MCPB for my project
work.
During this I'm getting the following error message.
Please suggest how to fix this problem and does it require reinstalling
AmberTools22.
(base) (base) [niperg.kaberi AD]$ MCPB.py -i 6Q2T.in -s 1
Traceback (most recent call last):
File "/home/software/amber22/bin/MCPB.py", line 34, in <module>
from pymsmt.mcpb.gene_model_files import get_ms_resnames,
gene_model_files
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mcpb/gene_model_files.py",
line 7, in <module>
from pymsmt.mol.pdbio import get_atominfo_fpdb, writepdbatm
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mol/pdbio.py",
line 5, in <module>
from pymsmt.mol.mol import Atom, Residue, Molecule, get_reslist
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mol/mol.py",
line 2, in <module>
from pymsmt.mol.element import resnamel
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mol/element.py",
line 5, in <module>
from parmed.periodic_table import AtomicNum
ModuleNotFoundError: No module named 'parmed'
(base) [niperg.kaberi AD]$ pdb4amber -i 6Q2T_H-dry.pdb -o 6Q2T_H-dry1.pdb
Traceback (most recent call last):
File "/home/software/amber22/bin/pdb4amber", line 33, in <module>
sys.exit(load_entry_point('pdb4amber==22.0', 'console_scripts',
'pdb4amber')())
File "/home/software/amber22/bin/pdb4amber", line 25, in
importlib_load_entry_point
return next(matches).load()
File
"/home/software/amber22/miniconda/lib/python3.9/importlib/metadata.py",
line 86, in load
module = import_module(match.group('module'))
File
"/home/software/amber22/miniconda/lib/python3.9/importlib/__init__.py",
line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed
File
"/home/software/amber22/lib/python3.9/site-packages/pdb4amber/__init__.py",
line 1, in <module>
from . import pdb4amber
File
"/home/software/amber22/lib/python3.9/site-packages/pdb4amber/pdb4amber.py",
line 7, in <module>
import parmed
ModuleNotFoundError: No module named 'parmed'
Thank you and best regards.
Ankita Nishad,
MS Pharm in Med Chem,
NIPER Guwahati
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Received on Fri Aug 19 2022 - 21:30:04 PDT
