Hi,
Thank you for all your immediate replies.
I have completed the installation of Ambertools19. When I run
antechamber command I get the following error
antechamber -fi pdb -fo prepi -i DOX_H.pdb -o DOX_H_clean.prepi -c bcc
-pf y
Welcome to antechamber 19.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Info: Bond types are assigned for valence state (3) with penalty (1).
Info: Total number of electrons: 285; net charge: 0
Info: The number of electrons is odd (285).
Please check the total charge (-nc flag) and spin multiplicity (-m
flag).
Running: /home/gauri/Software/amber18/bin/sqm -O -i sqm.in -o sqm.out
/home/gauri/Software/amber18/bin/to_be_dispatched/antechamber: Fatal
Error!
Also while running pdb4amber command, I am getting the following error:
Traceback (most recent call last):
File "/home/gauri/Software/amber18/bin/pdb4amber", line 11, in
<module>
load_entry_point('pdb4amber==1.7.dev0', 'console_scripts',
'pdb4amber')()
File
"/home/gauri/Software/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/home/gauri/Software/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 2843, in load_entry_point
return ep.load()
File
"/home/gauri/Software/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 2434, in load
return self.resolve()
File
"/home/gauri/Software/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 2440, in resolve
module = __import__(self.module_name, fromlist=['__name__'],
level=0)
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/pdb4amber-1.7.dev0-py2.7.egg/pdb4amber/__init__.py",
line 1, in <module>
from . import pdb4amber
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/pdb4amber-1.7.dev0-py2.7.egg/pdb4amber/pdb4amber.py",
line 7, in <module>
import parmed
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/__init__.py",
line 22, in <module>
from parmed import unit, utils
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/unit/__init__.py",
line 27, in <module>
from parmed.unit.unit import Unit, is_unit
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/unit/unit.py",
line 35, in <module>
from parmed.utils.six import iterkeys
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/utils/__init__.py",
line 3, in <module>
from parmed.utils.pairlist import find_atom_pairs
File
"/home/gauri/Software/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/utils/pairlist.py",
line 5, in <module>
import numpy as np
ImportError: No module named numpy.
Thank you
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 14 2019 - 05:00:02 PDT
