<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">Hi, </span><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">I used gromacs package (ver 4.0.3) for energy minimization of protein homology model.</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">After em, some residues were mangled if I see structure using jV protein structure view (<a href="http://www.pdbj.org/jv/index.html" target="_blank" style="color: rgb(17, 37, 8); ">http://www.pdbj.org/jv/index.<wbr>html</a>) and rasmol.</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">Especially, some glycine were disappeared on jV viewer and rasmol. </div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">It maybe because that distance between two atoms are far apart, I think.</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">I used em.mdp and commands for em like below and I attached pdb file of mangled region:</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">EM.mdp</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; ">==</div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><div>cpp = /usr/bin/cpp</div><div>define = -DFLEX_SPC</div><div>constraints = none</div><div>integrator = steep</div><div>dt = 0.002</div><div>nsteps = 5000</div><div>emtol = 1000</div><div>emstep = 0.01</div><div>nstcomm = 1</div><div>ns_type = grid</div><div>nstlist = 1</div><div>rlist = 1.2</div><div>coulombtype = PME</div><div>rcoulomb = 1.2</div><div>rvdw = 1.2</div><div>pbc = xyz</div></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><br></div><div style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><div>$ pdb2gmx -nointer -ff G43a1 -ignh -missing -f min_struct.pdb -p min_struct -o min_struct -i min_struct</div><div>$ grompp -f min_struct_scaffold_1 -c min_struct -n min_struct -p min_struct -o min_struct</div><div>$ mdrun -nice 0 -s min_struct -o min_struct -c min_struct_out.pdb -e min_struct -g min_struct.log</div><div><br></div><div></div></div><br><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; "><div><div> </div></div></span></body></html>