#!/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 # !! *** same procedure as in TM31_sol, now with polarized ff *** !! # used TM31 created in moe, then sed chain name in pymol using # alter (all),chain='A' # sort # Problem with protonated Aspartate. Is not supported, but is basically the same as a cysteine residue. # Therefore mutated aa form of TM31C to TM31C_D14C # then make martini topology on labtop: # ./martinize.py -f TM31C_D14C_E19C.pdb -o system_vaccum.top -x TM31C_D14C_E19C_pol_CG.pdb -dssp /Applications/DSSP_MAC.EXE -p backbone -ff martini22p # then modified both TM31C_D14C_E19C_pol_CG.pdb to TM31CproDproE_pol_CG.pdb and Protein_A.itp by changing Cys into Asp0 and Glu0 settings editconf -f TM31CproDproE_pol_CG.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 20 mdrun -deffnm minimization_vaccum -v #after minimization, rotate to align with z-axis membrane editconf -f minimization_vaccum.gro -princ -o minimization_vaccum_rotate.gro -rotate 0 80 0 #and put into membrane (allow large box to accomodate 31 residue peptide) ./insane.py -f minimization_vaccum_rotate.gro -o system.gro -pbc optimal -box 6.9,6.9,11 -l POPC:7 -l CHOL:3 -u POPC:7 -u CHOL:3 -center -sol PW #ensure following ratio in system.gro! #POPC 53 #CHOL 23 #POPC 53 #CHOL 23 #due to ASP0 and GLU0, system is not neutral, so let's neutralize: grompp -f genion.mdp -c system.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 # index file necessary to use as input with grompp, POPC_CHOL needs to be specified as one temperature coupling group, mdp files were modified accordingly # also correct ASP0 and GLU0, need to be part of Protein # finally, PW and CL- need to be combined as well make_ndx -f system_neutral.gro -o index.ndx <