Difference between revisions of "Molecular Dynamics Simulations"
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*In this step we added restrains to disable very fast vibrations such as seen for hydrogen atoms to reduce the simulation time. The command we used was <code>genrestr -f 1a6z_solv2.pdb -o 1a6z.itp</code> |
*In this step we added restrains to disable very fast vibrations such as seen for hydrogen atoms to reduce the simulation time. The command we used was <code>genrestr -f 1a6z_solv2.pdb -o 1a6z.itp</code> |
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Revision as of 13:03, 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
Genion is used with genion -s 1a6z_final_box_water.tpr -o 1a6z_solv.pdb -conc 0.1 -neutral -pname NA+ -nname CL-
Now we counted the added ions by using tr -s ' ' '\n' < out.txt | grep -c 'ION'. ION is set to NA+ and CL- to get the number of added ions. For CL- genion added 41 and for NA+ genion added 52 ions.
- the Next step was to edit the SOL entry in the .top file. Here we found a SOL entry of 21363 which we changed to 21363-52-41=21270 and added two new entrys, NA with the value 52 and CL with the value 41.
- After adding the new water, we checked for an overlab with the crystal waterby using
repairPDB 1a6z_solv.pdb -cleansol > 1a6z_solv2.pdb, but as we had no crystal water in our file, we assumed to have no overlab. And as we found no REMARK tag in the new file, we should have no overlab.
- In this step we added restrains to disable very fast vibrations such as seen for hydrogen atoms to reduce the simulation time. The command we used was
genrestr -f 1a6z_solv2.pdb -o 1a6z.itp
