#!/bin/bash # # Code by venkentom@gmail.com # # Licenced by the GPL General Public License # Have a look at: # http://www.gnu.org/copyleft/gpl.html # For more information about the GPL License # # I am not responsible for what this code does to your hw/sw/mind # Use at your own risk # #Put gromacs commands after this line DIR=`pwd` #Config NPROCS=2 # not possible to automatically create TM19 containing protonated aspartate using martinize.py, so manual procedure needed # starting from TM19 -> convert into TM19_C14 using moe (parameters of cys are quite close to asp0) # then sed chain name in pymol using # alter (all),chain='A' # sort # then make martini topology: ./martinize.py -f TM19_C14_sed.pdb -o system_vaccum.top -x TM19_C14_pol_CG.pdb -dssp /Applications/DSSP_MAC.EXE -p backbone -ff martini22p #manually adapt TM19_C14_pol_CG.pdb into TM19_D0.pdb and change Protein_A.itp! #editconf -f TM19_D0.pdb -o editconf.pdb -bt cubic -d 1 -c #change martini.itp to #include "martini_v2.2.itp" in system_vaccum.top #grompp -f minimization_vaccum.mdp -p system_vaccum.top -c editconf.pdb -o minimization_vaccum.tpr -maxwarn 1 #mdrun -deffnm minimization_vaccum -v editconf -f TM19_D0.pdb -o editconf.gro -box 9 9 9 genbox -cp editconf.gro -ci popc_single.gro -nmol 128 -try 500 -o genbox.gro grompp -f minimization.mdp -c genbox.gro -p system.top -maxwarn 10 -o min-init.tpr mdrun -deffnm min-init -v genbox -cp min-init.gro -cs polarize-water.gro -o waterbox.gro -maxsol 1500 -vdwd 0.21 #due to protonated asp, neutralization needed!! grompp -f genion.mdp -c waterbox.gro -p system.top -o system_neutral.tpr genion -s system_neutral.tpr -o system_neutral.gro -p system.top -pname NA- -nname CL- -neutral -conc 0.000001 << EOL PW EOL #add #include "martini_v2.0_ions.itp" to system.top! grompp -f minimization.mdp -c system_neutral.gro -p system.top -maxwarn 10 -o min-solvent.tpr mdrun -deffnm min-solvent -v make_ndx -f system_neutral.gro -o index.ndx <