Gaussian09 bug fix

Thanks to Jordi, we could find a solution to this gaussian bug: (I wanted to parametrize a compound with iop(6/33=2) which has been deleted in our marc g09 version)

http://ambermd.org/bugfixesat.html

Gaussian 09 fix

In Gaussian09 rev B.01, the facility to write out the electrostatic potential on a grid of points was inadvertently deleted. This means that antechamber and resp jobs won't work as they should. Fernando Clemente of Gaussian has kindly provided a script to work around the problem. Download the fixreadinesp.sh file, and follow the instructions there. (Note: you will have to make the script executable by typing chmod +x fixreadinesp.sh.)

#!/bin/bash

######################################################################

# "fixreadinesp.awk" by Fernando R. Clemente (Gaussian, Inc.)

# Workaround for G09 rev. B.01 not printing the list of

# electrostatic potential values at the grid points in

# "Pop=ESP" jobs with "IOp(6/33=2)":

# 1) Run the "Pop=ESP" jobs with "IOp(6/33=2)" as you would

# normally do.

# 2) Run this script on the output of job 1) and redirect to

# a new Gaussian input file. This will extract the list of

# grid points and setup a new job in which this list is given

# explicitly in the input file. This second Gaussian job

# uses the results saved in the checkpoint file of job 1),

# so the QM calculation does not need to be redone. Example:

# fixreadinesp.sh output.log > readincenters.com

# 3) Run the new Gaussian job with the generated input file in

# step 2) in order to obtain a G09 output file that contains

# the values of the electrostatic potential at each grid point.

# 4) Re-run this script on the G09 output file generated by step 3)

# to fix the format so "espgen" is able to read this type of

# Gaussian output file. Example:

# fixreadinesp.sh readincenters.log > fixed.log

# This final Gaussian output file should work with "espgen".

######################################################################

# Extracts list of grid points from a G09 output file

# and sets up an Gaussian input file to re-run the job

# with the list of points given explicitly.

if [ "$(grep "Charges from ESP fit" ${1})" != "" ] ; then

printf "%s\n" "$(grep -i "%chk=" ${1})"

printf "#p geom=allcheck chkbas guess=(read,only) density=check\n"

printf "nosymm prop=(potential,read) pop=minimal\n\n"

grep "ESP Fit Center" ${1} | cut -c32- -

printf "\n"

else

# Fixes the output of a G09 job with

# read-in values to make "espgen" be

# able to recognize the list of centers

# and the electrostatic potential values.

awk '

{

if ($0 ~ /Electric Field/) {

while ($0 !~ /Atom/) { print $0 ; getline }

while ($0 ~ /Atom/) { print $0 ; getline }

while ($0 !~ /^ ------/) {

CENTERID=$1

OLDSTR=sprintf("%i ",CENTERID)

NEWSTR=sprintf("%i Fit",CENTERID)

sub(OLDSTR,NEWSTR,$0)

print $0

getline

}

sub(/Read-in Center/,"ESP Fit Center",$0)

print $0

}' ${1}

######################################################################

#!/bin/bash

######################################################################

# "fixreadinesp.awk" by Fernando R. Clemente (Gaussian, Inc.)

# Workaround for G09 rev. B.01 not printing the list of

# electrostatic potential values at the grid points in

# "Pop=ESP" jobs with "IOp(6/33=2)":

# 1) Run the "Pop=ESP" jobs with "IOp(6/33=2)" as you would

# normally do.

# 2) Run this script on the output of job 1) and redirect to

# a new Gaussian input file. This will extract the list of

# grid points and setup a new job in which this list is given

# explicitly in the input file. This second Gaussian job

# uses the results saved in the checkpoint file of job 1),

# so the QM calculation does not need to be redone. Example:

# fixreadinesp.sh output.log > readincenters.com

# 3) Run the new Gaussian job with the generated input file in

# step 2) in order to obtain a G09 output file that contains

# the values of the electrostatic potential at each grid point.

# 4) Re-run this script on the G09 output file generated by step 3)

# to fix the format so "espgen" is able to read this type of

# Gaussian output file. Example:

# fixreadinesp.sh readincenters.log > fixed.log

# This final Gaussian output file should work with "espgen".

######################################################################

# Extracts list of grid points from a G09 output file

# and sets up an Gaussian input file to re-run the job

# with the list of points given explicitly.

if [ "$(grep "Charges from ESP fit" ${1})" != "" ] ; then

printf "%s\n" "$(grep -i "%chk=" ${1})"

printf "#p geom=allcheck chkbas guess=(read,only) density=check\n"

printf "nosymm prop=(potential,read) pop=minimal\n\n"

grep "ESP Fit Center" ${1} | cut -c32- -

printf "\n"

else

# Fixes the output of a G09 job with

# read-in values to make "espgen" be

# able to recognize the list of centers

# and the electrostatic potential values.

awk '

{

if ($0 ~ /Electric Field/) {

while ($0 !~ /Atom/) { print $0 ; getline }

while ($0 ~ /Atom/) { print $0 ; getline }

while ($0 !~ /^ ------/) {

CENTERID=$1

OLDSTR=sprintf("%i ",CENTERID)

NEWSTR=sprintf("%i Fit",CENTERID)

sub(OLDSTR,NEWSTR,$0)

print $0

getline

}

sub(/Read-in Center/,"ESP Fit Center",$0)

print $0

}' ${1}

######################################################################

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fixreadinesp.sh_.gz	1.03 KB

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