Difference between revisions of "Molecular Dynamics Simulations"
From Bioinformatikpedia
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Then a box around our protein was added by <code>editconf -f 1a6z_final.gro -o 1a6z_final_box.gro -bt dodecahedron -d 1.0</code><br> |
Then a box around our protein was added by <code>editconf -f 1a6z_final.gro -o 1a6z_final_box.gro -bt dodecahedron -d 1.0</code><br> |
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and filled this box with water by using <code>genbox -cp 1a6z_final_box.gro -cs spc216.gro -p 1a6z_final.top -o 1a6z_final_box_water.gro</code> |
and filled this box with water by using <code>genbox -cp 1a6z_final_box.gro -cs spc216.gro -p 1a6z_final.top -o 1a6z_final_box_water.gro</code> |
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| + | Now we create the .tpr file for further use with genion by <code>grompp -v -f first.mdp -c 1a6z_final_box_water.gro -p 1a6z_final.top -o 1a6z_final_box_water.tpr</code> |
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Revision as of 12:34, 6 July 2011
Preparation
- We extracted all crystal water by
repairPDB 1a6z.pdb -ssw 15t >ssw.tmpbut, 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
Now we create the .tpr file for further use with genion by grompp -v -f first.mdp -c 1a6z_final_box_water.gro -p 1a6z_final.top -o 1a6z_final_box_water.tpr
