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--- adjusting_water_level_mutating_residues_of_existing_simulations [2021/11/10 19:24] – created edit
+++ adjusting_water_level_mutating_residues_of_existing_simulations [2021/11/10 19:29] (current) – edit
@@ Line 1: / Line 1: @@
 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.
   - Download and open the PDB in VMD
@@ Line 12: / Line 12: @@
      cd Desktop
      $smd writepdb less_water.pdb
   - Find the edited PDB on the desktop
   - 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
   - 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
   - On the appropriate screen select "rename" to rename the different components to the original names
@@ Line 28: / Line 29: @@
-To Mutate an Amino Acid (Mahdi)
+**To Mutate an Amino Acid (Mahdi)**
   - Start with a PDB file of a given equilibrated simulation
   - Upload this PDB to CHARMM-GUI
   - 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 "mutate" to mutate all the different residues, should be one of the first screens
   - Be sure to preserve any disulfide bonds... check everything
   - Select the "rename" option to essentially allow the various components to be recognized by the computer