asking gpt for an oxygen molecule

oxy.sh

using python and mogli code a complete app whose output is the rendering of an oxygen molecule. Generate required xyz files via a shell script in bash.

#!/bin/bash

#PBS -l nodes=1:ppn=1

#PBS -l walltime=48:00:00

#PBS -l mem=1gb

#PBS -N oxygen

#PBS -j oe

#PBS -o /home/user/oxygen.out

#PBS -e /home/user/oxygen.err

cd $PBS_O_WORKDIR

/path/to/python /path/to/mogli/code/oxygen.py



generate required xyz files to render an oxygen molecule in mogli via a shell script in bash.

create three files:

touch oxygen.xyz
touch render.sh
touch oxygen.pdb

in oxygen.xyz, put:

8

Oxygen

O      0.000000      0.000000      0.000000
H      0.000000      0.000000      1.080000
H      1.080000      0.000000      0.000000

in render.sh, put:

#!/bin/bash

mogli oxygen.xyz

in oxygen.pdb, put:

ATOM      1  O           0       0.000   0.000   0.000  1.00  0.00           O  
ATOM      2  H           0       0.000   0.000   1.082  1.00  0.00           H  
ATOM      3  H           0       1.082   0.000   0.000  1.00  0.00           H