| Hi, I used gromacs package (ver 4.0.3) for energy minimization of protein homology model. After em, some residues were mangled if I see structure using jV protein structure view (http://www.pdbj.org/jv/index. Especially, some glycine were disappeared on jV viewer and rasmol. It maybe because that distance between two atoms are far apart, I think. I used em.mdp and commands for em like below and I attached pdb file of mangled region: EM.mdp == cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 nsteps = 5000 emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid nstlist = 1 rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz $ pdb2gmx -nointer -ff G43a1 -ignh -missing -f min_struct.pdb -p min_struct -o min_struct -i min_struct $ grompp -f min_struct_scaffold_1 -c min_struct -n min_struct -p min_struct -o min_struct $ mdrun -nice 0 -s min_struct -o min_struct -c min_struct_out.pdb -e min_struct -g min_struct.log |
mangled_region.pdb
Description: Binary data
-- Taeho Kim (Ph.D) PostDoctoral Researcher Systems Immunology Laboratory WPI Immunology Frontier Research Center Osaka University, Osaka, 565-0871, Japan email : t...@ifrec.osaka-u.ac.jp |
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