[gmx-users] spliting chains

özge kül ozgekul8233 at yahoo.com
Fri Mar 30 22:00:31 CEST 2007

  Thank you for your advices.The A-chain is topologically similar to the activation peptide of chymotrypsin(ogen) and connected in a similar manner through the Cys1–Cys122 disulfide bridge to the B-chain. Most of the A-B chain interactions involve charged side chains; six are buried salt bridges, and 10 are involved in interchain hydrogen bonds .In VMD I saw the two chains split up at atime and then get together.I only know that I should  write -merge in pdb2gmx line.According to the informations above how can you help me?
  1.      pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o  1ppbfree.gro  -merge
  2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
  3.      genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
  4.      grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top
  5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr

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