Difference between revisions of "Molecular Dynamics Simulations"
From Bioinformatikpedia
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* <code>pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens</code> |
* <code>pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens</code> |
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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> |
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> |
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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> |
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Revision as of 12:25, 6 July 2011
Preparation
repairPDB 1a6z.pdb -ssw 15t >ssw.tmpbut there was no crystal water included.repairPDB 1a6z.pdb -nosol >1a6z_clean.pdbscwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.logrepairPDB 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
