using Jan's code to generate and evaluate an esp from given partial charges on a particular mesh

introduction

we want to create esp cube files from given partial charges and compare these
to compare cube files they must have the same internal structure (ie same number of points)
see the wiki and gaussian website for cubegen "http://gaussian.com/cubegen/" and cubman "http://gaussian.com/cubman/" for more info on generating gaussian cubes with the same structure
here we will be using one cube file as a template for the one to be produced thus allowing for comparison
the best comparison point is the "real" esp created earlier ie the gaussian cube generated esp file

create our own ESP from given partial charges and mesh

the script we need is rep_esp.py
creates a gaussian cube file of the esp
for instructions run with -h argument "rep_esp.py -h"
required arguments are

input charge type=name the charges to be extracted options are 'mulliken', 'nbo', 'aim', 'mk', 'chelp', 'chelpg', 'hly', or 'list' if the charges are to be provided from a text file

input charge file = file to extract charges from this can be a gaussian.log file or a text file if you have used resp

template cube file = name of file with a template esp, this is necessary to compare the cube files

then add -o file to direct the output to a named cube file (remove the .cub extension)
for example creating a cube file from the gaussian mk charges, and the resp_mk charges

rep_esp.py mk ch3oh_mk.log ch3oh_esp.cub -o ch3oh_mk_esp
rep_esp.py list resp_charges_mk.txt ch3oh_esp.cub -o ch3oh_resp_mk_esp

compare our ESP files

we want to compare the partial charge derived esp cube files to the "proper" esp obtained from the electronic density
for this we use field_diff.py
required arguments are

input cube file=real esp cube file file.cub

input charge file = file to extract charges from this can be a gaussian.log file or a text file if you have used resp

template cube file = name of file with a template esp, this is necessary to compare the cube files

options include

"-o filename" (remove the .cub extension) to direct the output to a named cube file

"--absolute" to get the absolute error (ie all positive)

"--relative" to get the relative value ie the error divided by the value of the field at this point some problems here!

"--exclude density.cub iso-value distance" to exclude points lying closer than the electron density iso-surface given,

for this you need to specify an electron density cube denisty.cube, an iso-value and a distance?

field_diff.py ch3oh_esp.cub ch3oh_resp_mk_esp.cub -o ch3oh_real_vs_resp_mk_diff_esp
open the cub file in gaussview and play around with the iso-surface values starting with 0.004 is a good option here I have compared the real esp and the esp generated from the equivalenced mk charges, remember this is a difference!	esp 0.004 difference iso-surface for ch3oh
field_diff.py --exclude ch3oh_den.cub 0.008 0.001 ch3oh_esp.cub ch3oh_resp_mk_esp.cub -o ch3oh_real_vs_resp_mk_exclude_diff_esp
not sure what use this is but excluded within the 0.008 density sphere (this contour is shown in slightly deeper colour) rest is a contour plot of the esp difference and the 3D is the difference iso-surface at 0.004	esp difference with exclusion zone for ch3oh