[AMBER] sqm error

From: <174026008.iitb.ac.in>
Date: Sat, 14 Sep 2019 17:21:44 +0530


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

Running: /home/gauri/Software/amber18/bin/sqm -O -i sqm.in -o sqm.out
/home/gauri/Software/amber18/bin/to_be_dispatched/antechamber: Fatal

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
    load_entry_point('pdb4amber==1.7.dev0', 'console_scripts',
line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
line 2843, in load_entry_point
    return ep.load()
line 2434, in load
    return self.resolve()
line 2440, in resolve
    module = __import__(self.module_name, fromlist=['__name__'],
line 1, in <module>
    from . import pdb4amber
line 7, in <module>
    import parmed
line 22, in <module>
    from parmed import unit, utils
line 27, in <module>
    from parmed.unit.unit import Unit, is_unit
line 35, in <module>
    from parmed.utils.six import iterkeys
line 3, in <module>
    from parmed.utils.pairlist import find_atom_pairs
line 5, in <module>
    import numpy as np
ImportError: No module named numpy.

Thank you
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Received on Sat Sep 14 2019 - 05:00:02 PDT
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