Difference between revisions of "Molecular Dynamics Simulations"

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(Preparation)
(Preparation)
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==Preparation==
 
==Preparation==
* <code>repairPDB 1a6z.pdb -ssw 15t >ssw.tmp</code> but there was no crystal water included.
+
* We extracted all crystal water by <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>
+
* Extracting the pure protein by <code>repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb</code>
* <code>scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log</code>
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* Complete missing side chains with <code>scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log</code>
* <code>repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb</code>
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* Remove all H-Atoms by <code>repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb</code>
 
* because there was no crystal water in the origin pdb included, we had nothing to concatenate.
 
* because there was no crystal water in the origin pdb included, we had nothing to concatenate.
   

Revision as of 12:33, 6 July 2011

Preparation

  • We extracted all crystal water by repairPDB 1a6z.pdb -ssw 15t >ssw.tmp but, there was no crystal water included.
  • Extracting the pure protein by repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb
  • Complete missing side chains with scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log
  • Remove all H-Atoms by 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.

Creation of the gromac files

  • pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens

Then a box around our protein was added by editconf -f 1a6z_final.gro -o 1a6z_final_box.gro -bt dodecahedron -d 1.0
and filled this box with water by using genbox -cp 1a6z_final_box.gro -cs spc216.gro -p 1a6z_final.top -o 1a6z_final_box_water.gro