Difference between revisions of "Molecular Dynamics Simulations"
From Bioinformatikpedia
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==Preparation== |
==Preparation== |
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| − | * <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> |
+ | * 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> |
+ | * 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. |
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Revision as of 12:33, 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
