Hi,<br><br>I used a script given below for energy minimization of a native protein-protein complex 1akj.<br><br>I removed HETATMs and water molecules from the structure, and the minimized structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.<br>
Then I used rasmol to check the result. The ligand is ran away from receptor.<br> rasmol 1akj_oplsaa.minim_traj.pdb<br><br><br>Then I tried the larger epsilon_r = 800000.0, and got very similar result. I mean that for two substantially different values of the epsilon_r minimization gives absolutely the same final positions of the ligand.<br>
<br>I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1, G45a3, G53a5, G53a6, gmx, oplsaa.<br>I also got similar result.<br><br><br>script: <br><br>pdb2gmx -ff oplsaa -f 1akj_oplsaa.pdb -p 1akj_oplsaa.top -o 1akj_oplsaa.gro -i 1akj_oplsaa.itp > 1akj_oplsaa.<br>
output.pdb2gmx 2>&1 &<br><br>grompp -f em.mdp -c 1akj_oplsaa.gro -p 1akj_oplsaa.top -o 1akj_oplsaa.input.tpr > 1akj_oplsaa.output.grompp<br>2>&1 &<br><br>mdrun -nice 0 -v -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.trr -c 1akj_oplsaa.minimized.gro -e<br>
1akj_oplsaa.<br><br>minim_ener.edr > 1akj_oplsaa.output.mdrun 2>&1 &<br><br> trjconv -f 1akj_oplsaa.minim_traj.trr -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.pdb << HHH<br>2<br>2<br>HHH<br><br>
<br>em.mdp is :<br><br>title = 1akj_oplsaa<br>cpp = /usr/bin/cpp<br>define = -DFLEX_SPC<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>
nsteps = 100<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = cut-off<br>epsilon_r = 80.0<br>rcoulomb = 1.8<br>vdwtype = cut-off<br>
rvdw = 1.8<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 10.0<br>emstep = 0.01<br><br><br><br><br clear="all"><br>-- <br>Shiyong Liu<br>Research Assistant<br>center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:        (785) 864-1962