rm -fR HFSTO3G HFSTO3G_temp" or use "charges -l list -c project_name
rm -fR HFSTO3G HFSTO3G_temp
rm -fR HF631GH HF631GH_temp
rm -fR B3LYPSTO3G B3LYPSTO3G_temp
rm -fR B3LYP631GH B3LYP631GH_temp
do_charges
module add openbabel:
module add gaussian:
do_charges
jmc
mc
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates > stat
head stat
head -n 20 stat
head -n 100 stat
cd pka
ls
cd phenols/
ls
cd corina/
ls
cd gaussian
ls
rm -fR HFSTO3G HFSTO3G_temp
rm -fR B3LYP631GH B3LYP631GH_temp
rm -fR B3LYPSTO3G B3LYPSTO3G_temp
rm -fR HFSTO3G HFSTO3G_temp
ls
module add openbabel:
cat list_head | while read i; do babel -ig09 $i/$i.log -osdf $i.sdf;done
ls
do_charges
rm -fR B3LYP631GH B3LYP631GH_temp
ls
rm -fR HF631GH HF6313GH_temp
ls
rm -fR HF631GH HF631GH_temp
ls
module add gaussian:
do_charges
cd pka/phenols/corina/gaussian
do_statistics
cd B3LYP631GH
~/benzoic_acids/statistics 
ls
cd pka
l
ls
cd phenols/
cd ../benzoic_acids/
ls
~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/
~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/; ~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/
~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/; ~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/; ~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/
~/benzoic_acids/table.py balloon_meta_para/; ~/benzoic_acids/table.py balloon_meta_para/MMFF94/; ~/benzoic_acids/table.py balloon_meta_para/gaussian/; ~/benzoic_acids/table.py corina_meta_para/; ~/benzoic_acids/table.py corina_meta_para/MMFF94/; ~/benzoic_acids/table.py corina_meta_para/gaussian/; ~/benzoic_acids/table.py openbabel_meta_para/; ~/benzoic_acids/table.py openbabel_meta_para/MMFF94/; ~/benzoic_acids/table.py openbabel_meta_para/gaussian/
~/benzoic_acids/table.py balloon_ortho/; ~/benzoic_acids/table.py balloon_ortho/MMFF94/; ~/benzoic_acids/table.py balloon_ortho/gaussian/; ~/benzoic_acids/table.py corina_ortho/; ~/benzoic_acids/table.py corina_ortho/MMFF94/; ~/benzoic_acids/table.py corina_ortho/gaussian/; ~/benzoic_acids/table.py openbabel_ortho/; ~/benzoic_acids/table.py openbabel_ortho/MMFF94/; ~/benzoic_acids/table.py openbabel_ortho/gaussian/
cd ..
cd anilines/
ls
table.py balloon 1
table.py balloon 0
table.py balloon 0; table.py balloon/MMFF94/ 0; table.py balloon/gaussian/ 0; table.py corina/ 0; table.py corina/MMFF94/ 0; table.py corina/gaussian/ 0; table.py openbabel/ 0; table.py openbabel/MMFF94/ 0; table.py openbabel/gaussian/ 0
table.py balloon 1; table.py balloon/MMFF94/ 1; table.py balloon/gaussian/ 1; table.py corina/ 1; table.py corina/MMFF94/ 1; table.py corina/gaussian/ 1; table.py openbabel/ 1; table.py openbabel/MMFF94/ 1; table.py openbabel/gaussian/ 1
module add pymo
module add pymol
pymol
ls
cd benzoic_acids/
ls
vi just_do_it.py 
module add gnuplot:
cd ..
ls
benzoic_acids/just_do_it.py 
vi benzoic_acids/just_do_it.py 
cat benzoic_acids/just_do_it.py 
echo #!/usr/bin/python
# -*- coding: utf-8 -*-
# just_do_it.py
import sys
exit
exit
ls | head
ls | head -n 50
ls | head -n 60
ls | head -n 80
cd tomasb
mc
ls
cd n19n
ls
cd share
ls
cd C04_pKa/
cd ..
cd software/
ls
cat analyze-separation-H
ls
cd 2010/
ls
cd bin
ls
cd ..
ls
cat ext_charges.pl 
cd ..
ls
cat ext_charges.pl
cat ext_charges.pl
ls
cd ../..
ls
cd ..
ls
cd tbouchal
ls
cd charges
ls
cd cc
ls
cd ..
cd ..
cd cc
ls
cd ..
ls
cd nci
ls
cd ..
ls
cd shared
ls
cd ..
ls
cd storage
ls
cd scripts/
ls
cd ..
ls
cd 5_methods/
ls
cd ..
ls
cd methods/
ls
cd ..
ls
cd H_charge/
ls
cd sdf
ls
cd hf_631gh
ls
cd ..
cd ..
cd ..
ls
cd ..
mc
cd ..
cd standag/
exit
exit
exit
exit
exit
exit
ls
vi just_do_it.py 
ls
cd benzoic_acids/
vi
vi acids.py
cd ..
module add gnuplot:
python just_do_it.py 
chmod 777 benzoic_acids/acids.py 
benzoic_acids/acids.py 
mc
ls
vi statistics 
cd phenols
cd pka
cd phenols
ls
cd balloon/
ls
cd gaussian
ls
cd HF631GH
ls
~/statistics
ls
mc
/home/bates/statistics
mc
ls
cd ..
cd ..
cd ..
cd ..
cd ..
ls
cd bin
vi analyze
ls
cd ..
ls
chmod 777 analyze 
ls
vi statistics 
cd pka/phenols/corina/gaussian
cd HF631GH
ls
~/statistics
                       mc
~/statistics
                       mc
~/statistics
                       mc
mc
~/statistics
mc
mc
4
exit
exit
exit
exit
ls
cat statistics
cd bin
cat statistics
ls
cat stat
rm stat
ls
vi statistics
cd pka
ls
cd phenols/
ls
cd corina/
ls
cd HF631GH
ls
python
python
python
cd ..
ls
cat NSC_95810.pka
cd gaussian
ls
cd HF631GH
~/statistics
mc7
mc
ls
~/statistics
mc
~/statistics
mc
ls
~/statistics
mc
~/statistics
cd ../B
cd ../B3LYP631GH
~/statistics
~/statistics; cd ../B3LYPSTO3G; ~/statistics; cd ../HFSTO3G; ~/statistics
cd ..
cd ..
cd ..
cd balloon/
cd gaussian
ls
cd B3LYP631GH; ~/statistics; cd ../B3LYPSTO3G; ~/statistics; cd ../HFSTO3G; ~/statistics; cd ../HF631GH; ~/statistics
cd ../../../openbabel/gaussian
cd B3LYP631GH; ~/statistics; cd ../B3LYPSTO3G; ~/statistics; cd ../HFSTO3G; ~/statistics; cd ../HF631GH; ~/statistics
ls
cd ..
ls
do_statistics
cd B3LYP631GH; ~/statistics; cd ../B3LYPSTO3G; ~/statistics; cd ../HFSTO3G; ~/statistics; cd ../HF631GH; ~/statistics
exit
mc
vi phenols.py 
ls
cat phenols.py 
ls
./phenols.py
vi phenols.py 
./phenols.py
module add gnuplot:
./phenols.py
cd pka/phenols/
ls
cd balloon/
~/benzoic_acids/table.py
~/benzoic_acids/table.py .;
cd ..
~/benzoic_acids/table.py balloon;
~/benzoic_acids/table.py balloon; ~/benzoic_acids/table.py balloon/MMFF94; ~/benzoic_acids/table.py balloon/gaussian; ~/benzoic_acids/table.py corina; ~/benzoic_acids/table.py corina/MMFF94; ~/benzoic_acids/table.py corina/gaussian; ~/benzoic_acids/table.py openbabel; ~/benzoic_acids/table.py openbabel/MMFF94; ~/benzoic_acids/table.py openbabel/gaussian
~/benzoic_acids/table.py balloon; ~/benzoic_acids/table.py balloon/MMFF94; ~/benzoic_acids/table.py balloon/gaussian; ~/benzoic_acids/table.py corina; ~/benzoic_acids/table.py corina/MMFF94; ~/benzoic_acids/table.py corina/gaussian; ~/benzoic_acids/table.py openbabel; ~/benzoic_acids/table.py openbabel/MMFF94; ~/benzoic_acids/table.py openbabel/gaussian
cd
vi phenols.py 
./phenols.py
vi phenols.py 
./phenols.py
ls
cat just_do_it.py 
python just_do_it.py 
exit
exit
exit
exit
cd phenols.py 
cd pka/drugs/phenols/
ls
module add openbabel
mkdir smiles
cat listp | while read i; do babel -isdf $i.sdf -osmi smiles/$i.smi; done
mkdir openbabel; cat listp | while read i; do babel --gen3D -ismi smiles/$i.smi -omol openbabel/$i.sdf; done
ls
cd smiles/
ls
cat 9996.smi 
cat 100117.smi 
cat 121503.smi 
cat 121503.smi 
cat 125450.smi 
cat 455632.smi 
cat 522683.smi
cat 56781.smi
ls | wc -l
cd ../corina/
ls
cat ../listp | while read i; do babel -ipdb $i.pdb -osdf $i.sdf; done
module add gaussian
kinit
do_charges
mkdir MMFF94
cd ..
cd openbabel/
do_charges
qstat -u bates
mc
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
qstat -u bates
cd ..
cd corina/
ls
cd B3LYPSTO3G
ls
cd ..
sync_charges -p B3LYPSTO3G
cd B3LYPSTO3G
~/analyze
mc
~/analyze m
/home/bates/analyze m
mc
/home/bates/analyze m
/home/bates/analyze -c m
mc
eixt
exit
ls
cd pka/drugs/
ls
cd phenols/
ls
cd corina
ls
do_statistics
ls
cd B3LYP631GH
ls
~/analyze -c m
mc
mc
emacs
./statistics.pl
mc
cd pka
cd phenols/
ls
wc -l lsit
wc -l list
cd ..
cd anilines/
ls
wc -l list
cd balloon/
ls
ls *.sdf | wc -l
cd ..
cd ..
cd benzoic_acids/
ls
cat list
wc -l list_meta_para 
wc -l list_ortho 
cd..
cd ..
cd ..
ls
./phenols.py 
module add gnuplot
./phenols.py 
module add gnuplot
~/benzoic_acids/just_do_it.py 
~/benzoic_acids/acids.py 
module
module add python:2.7.1
~/benzoic_acids/just_do_it.py 
module remove
module remove python:
~/benzoic_acids/just_do_it.py 
~/benzoic_acids/just_do_it.py 
exit
exit
exit
exit
ls
cd pka
la
cd pka
ls
cd drugs/
ls
cd phenols/
ls
mc
ls
cd corina/
ls
cd HF631GH
ls
mc
ls
pwd
mc
ls
analyze
mc
~/analyze 
~/analyze -c m
~/statistics
ls
ls
cd pka
cd anilines/
ls
cd corina/
ls
ls *.sdf | wc -l
cd ..
cd ..
cd benzoic_acids/
ls
cat list
ls corina_meta_para/*.sdf > list
ls corina_ortho/*.sdf >> list
cat list
wc -l list
wc -l list_meta_para 
wc -l list_ortho 
cd ..
cd anilines/
ls
cd corina/
ls
cd HF631GH
ls
cd ortho/
ls
wc -l n-charges.predict 
cd ..
cd meta_para/
wc -l n-charges.predict 
cat /proc/cpuinfo
cd pka/drugs/phenols/
ls
cd corina/
ls
