GAML

bash_gaml_update.sh

#!/bin/bash


FORMAT_DES="; Deep Eutectic Solvent OPLS-DES force field
; Version 4/2021
; Orlando Acevedo
; Email: orlando.acevedo@miami.edu
; Contributors: X. Zhong
;
; Zhong, X.; Velez, C.; Acevedo, O.
; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations.
; J. Chem. Theory Comput. 2021, 17, (in press).
; doi: 10.1021/acs.jctc.1c00047.
;
; GROMACS 5.0.7 is recommended for the values given below"


FORMAT_SLV="; Zhong, X.; Velez, C.; Acevedo, O.
; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations.
; J. Chem. Theory Comput. 2021, 17, (in press).
; doi: 10.1021/acs.jctc.1c00047.
;
; GAML charges with OPLS-AA
; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/
; Jorgensen Lab @ Yale University
;
; GROMACS 5.0.7 is recommended for the values given below"


for t in $(ls)
do
    if [[ ! -d $t ]]; then continue; fi
    echo "processing $t"
    cd $t/

for i in $(ls | grep 'pdb')
do
    sed -i '3,14d' $i
    sed -i '3i\
REMARK Zhong, X.; Velez, C.; Acevedo, O.\
REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations.\
REMARK J. Chem. Theory Comput. 2021, 17, (in press).\
REMARK doi: 10.1021/acs.jctc.1c00047.\
REMARK\
REMARK GAML charges with OPLS-AA\
REMARK Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/\
REMARK Jorgensen Lab @ Yale University\
REMARK\
REMARK GROMACS 5.0.7 is recommended for the values given below' $i
    sed -i '1s/REMARK/TITLE /' $i
done


for i in $(ls | grep 'itp')
do
    sed -i '3,14d' $i
    sed -i '3i\
; Zhong, X.; Velez, C.; Acevedo, O.\
; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations.\
; J. Chem. Theory Comput. 2021, 17, (in press).\
; doi: 10.1021/acs.jctc.1c00047.\
;\
; GAML charges with OPLS-AA\
; Generated By LigParGen Server: http://zarbi.chem.yale.edu/ligpargen/\
; Jorgensen Lab @ Yale University\
;\
; GROMACS 5.0.7 is recommended for the values given below' $i

    
done
    cd ../


done




For_final_check="for i in $(ls); do if [[ ! -d $i ]]; then continue; fi; cd $i; echo "file $i";  head -n 30 $i.itp; read $tmp; head -n 30 $i.pdb; read $tmp; echo ''; cd ../; echo ''; echo ''; echo ''; done"