wrote and executed this script: #!/bin/bash ############################################################################### ## ## ## Hello! ## ## Please contact me if you have any questions ## ## Contact Info: ## ## email: edward.kj1299@hotmail.com ## ## ## ## Code Inspiration from Bevan Lab's Gromacs Tutorial ## ## ## ############################################################################### ################################### ##### PRE-GROMACS SETUP ##### ################################### #make your main directory - you can name it whatever you like (but avoid spaces) #inside that directory make these directories: 0_mdps #mandatory 1_pdb2gmx 2_middle 5_md_pull #mandatory #put all the mdp files in the 0_mdps directory. ################################### ##### pdb2gmx ##### ################################### gmx pdb2gmx -f 13merDNA_Mutant.pdb -ignh -o complex.gro #choose amber99SB #choose tip3p for water ################################### ##### Make clamp POSRES ##### ################################### gmx genrestr -f ssBNA9_fixed4_GMX.gro -o posre_ssBNA9_fixed4_GMX.itp -fc 1000 1000 1000 choose: 2 (BNA) ################################### ##### Combine ##### ################################### #combine the .gro files #make sure to change the number of atoms in the system #copy and paste the clamp atoms into the file #edit the ssBNA9_fixed4_GMX.itp #change the name under [ moleculetype ] name to BNA: [ moleculetype] ;name nrexcl BNA 3 #edit the topol.top file #add the following right before [ moleculetype]: ; Include ligand topology #include "ssBNA9_fixed4_GMX.itp" ; Ligand position restraints #ifdef POSRES #include "posre_ssBNA9_fixed4_GMX.itp" #endif #and add the BNA to the list of molecules at the bottom #like this: [ molecules ] ; Compound #mols DNA_chain_B 1 BNA 1 #Add the following to posre.itp (including the hashtags) #ifdef POSRES_B #include "posre_DNA_chain_B.itp" #endif ################################### ##### solvate ##### ################################### gmx editconf -f complex.gro -o newbox.gro -center 4.5 4.5 9 -box 9 9 11 -rotate 90 190 0 gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top #look at the pbc box in vmd with this command > pbc box ################################### ##### add ions ##### ################################### gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1 #select SOL # NaCl was used in the Tm value experimentation gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -o em.tpr gmx mdrun -v -tunepme -deffnm em #for optimization with mpi (Does not work for my system) gmx tune_pme -s em.tpr -g -mdrun 'gmx_mpi mdrun' -np 12 #for viewing purposes gmx trjconv -s em.tpr -f em.trr -o em_noPBC.xtc -pbc mol -ur compact # choose 11 for non-Water (but remember the waters # have to be removed from the .gro file as well) ################################### ##### Make INDEX ##### ################################### gmx make_ndx -f em.gro > 1 | 2 > q ################################### ##### NPT ##### ################################### gmx grompp -f npt.mdp -n index.ndx -c em.gro -p topol.top -o npt.tpr gmx mdrun -v -tunepme -deffnm npt #took about 10 minutes #for viewing purposes gmx trjconv -s npt.tpr -f npt.trr -o npt_noPBC.xtc -pbc mol -ur compact ################################### ##### Pulling ##### ################################### gmx grompp -f md_pull.mdp -c npt.gro -n index.ndx -p topol.top -t npt.cpt -o pull.tpr gmx mdrun -v -tunepme -s pull.tpr #pull takes approx. 60 minutes gmx trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep #choose system #for viewing purposes gmx trjconv -s pull.tpr -f traj_comp.xtc -o pull_noPBC.xtc -pbc mol -ur compact #to generate a pdb from a gro file without waters in vmd set selection [atomselect top "not water"] $selection writepdb npt_no_waters.pdb #to see box coordinates in vmd molinfo 0 get {a b c alpha beta gamma} ################################### ##### After Pull INDEX ##### ################################### gmx make_ndx -f npt.gro -o index2.ndx > del 6 > del 2 > q ################################### ##### ONECLICK SETUP ##### ################################### #edit the ONECLICK_pt1.pl script: #change the for loops to match the amount of conf$i.gro files produced #change the index.ndx input to the name of the index file used #now run the perl script perl oneclick_pt1.pl #look at the COMs in the summary_distances.dat after running the perl script #select the checkpoint numbers at certain COM intervals (ex. 0.2) #write them down in a text file in a row separated by a space #example: 121 140 200 216 270 300 #now run oneclick_pt2.sh - you can run this anywhere ./oneclick_pt2.sh #if there is a 'permission denied' run this: chmod 777 oneclick_pt2.sh #input the selected coordinates via copy and paste from the text file #took about 22 hours for umbrella sampling ################################### ##### FINAL ANALYSIS ##### ################################### #to correctly read the histogram xmgrace -nxy histo.xvg