Molecular Dynamics Simulations

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Revision as of 12:15, 6 July 2011 by Landerer (talk | contribs) (Created page with "==Preparation== * <code>repairPDB 1a6z.pdb -ssw 15t >ssw.tmp</code> but there was no crystal water included. * <code>repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb</code> * <code>scwr…")
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Preparation

  • repairPDB 1a6z.pdb -ssw 15t >ssw.tmp but there was no crystal water included.
  • repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb
  • scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log
  • repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb
  • because there was no crystal water in the origin pdb included, we had nothing to concatenate.
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