adjusting_water_level_and_mutating_residues_of_existing_simulations
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| adjusting_water_level_and_mutating_residues_of_existing_simulations [2021/11/10 19:32] – created edit | adjusting_water_level_and_mutating_residues_of_existing_simulations [2021/12/07 15:09] (current) – edit | ||
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| - Find the edited PDB on the desktop | - Find the edited PDB on the desktop | ||
| + | - Adjust the position of any ions to prevent a vacuum from being created | ||
| - Need to include all the sections of the simulation including all the different proteins or peptides or drugs or any other missing molecules | - Need to include all the sections of the simulation including all the different proteins or peptides or drugs or any other missing molecules | ||
| - Then upload to the CHARMM-GUI PDB reader | - Then upload to the CHARMM-GUI PDB reader | ||
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| - Use the Xmin and Xmax, Ymin... to get the lengths of the different axis | - Use the Xmin and Xmax, Ymin... to get the lengths of the different axis | ||
| - Update the number of waters now that it has been adjusted | - Update the number of waters now that it has been adjusted | ||
| + | - Delete the lines that correspond to the "# planar and Pulling restraints" | ||
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| - Select the " | - Select the " | ||
| - Continue through the steps to get the output and download it and pick up after the " | - Continue through the steps to get the output and download it and pick up after the " | ||
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adjusting_water_level_and_mutating_residues_of_existing_simulations.1636590735.txt.gz · Last modified: 2021/11/10 19:32 by edit