adjusting_water_level_mutating_residues_of_existing_simulations
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
adjusting_water_level_mutating_residues_of_existing_simulations [2021/11/10 19:25] – edit | adjusting_water_level_mutating_residues_of_existing_simulations [2021/11/10 19:29] (current) – edit | ||
---|---|---|---|
Line 1: | Line 1: | ||
Written By Robert | Written By Robert | ||
- | To Adjust the water level of the simulation (Robert): | + | **To Adjust the water level of the simulation (Robert):** |
- Generate a PDB of the simulation using the steps from the NAMD PMF section where the PDB of the adjusted simulation is generated. | - Generate a PDB of the simulation using the steps from the NAMD PMF section where the PDB of the adjusted simulation is generated. | ||
- Download and open the PDB in VMD | - Download and open the PDB in VMD | ||
Line 19: | Line 19: | ||
- Then upload to the CHARMM-GUI PDB reader | - Then upload to the CHARMM-GUI PDB reader | ||
- Be sure to keep certain options like the terminal group patching consistent | - Be sure to keep certain options like the terminal group patching consistent | ||
- | - Be sure to select mutate the residue on one of the first option screenes | ||
- Be sure to preserve any disulfide bonds... check everything | - Be sure to preserve any disulfide bonds... check everything | ||
- On the appropriate screen select " | - On the appropriate screen select " | ||
Line 30: | Line 29: | ||
- | To Mutate an Amino Acid (Mahdi) | + | **To Mutate an Amino Acid (Mahdi)** |
- Start with a PDB file of a given equilibrated simulation | - Start with a PDB file of a given equilibrated simulation | ||
- Upload this PDB to CHARMM-GUI | - Upload this PDB to CHARMM-GUI | ||
- Be sure to keep certain options like the terminal group patching consistent | - Be sure to keep certain options like the terminal group patching consistent | ||
- | - Be sure to select mutate the residue on one of the first option screenes | + | - Be sure to select |
- Be sure to preserve any disulfide bonds... check everything | - Be sure to preserve any disulfide bonds... check everything | ||
- Select the " | - Select the " |
adjusting_water_level_mutating_residues_of_existing_simulations.1636590311.txt.gz · Last modified: 2021/11/10 19:25 by edit