Re: [AMBER] sqm error

From: David Case <>
Date: Sat, 14 Sep 2019 16:28:55 +0000

On Sat, Sep 14, 2019, 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:
>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)?


AMBER mailing list
Received on Sat Sep 14 2019 - 09:30:01 PDT
Custom Search