On Sat, Sep 14, 2019, 174026008.iitb.ac.in wrote:
>
>antechamber -fi pdb -fo prepi -i DOX_H.pdb -o DOX_H_clean.prepi -c bcc
>-pf y
>
>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
You either have a bad structure or the wrong net charge. Hard to say
which.... Antechamber charge estimatation only works for closed-shell
molecules, with an even number of electrons.
>
>Also while running pdb4amber command, I am getting the following error:
>
>"/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.
What python are you using? Did you accept the offer to install a
miniconda version (which will have numpy available)?
....dac
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Received on Sat Sep 14 2019 - 09:30:01 PDT
