Klauda Lab Simulation Wiki

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Written By 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
  - Use the code below and adjust the -50 and 35 to get the right water level. Less water will speed the simulation.

     set smd [atomselect top "segname IONS or protein or segname MEMB or water and same residue as ( name H1 and z >-50 and z <35) and water and 
     same residue as ( name H2  and z >-50 and z <35) and water and same residue as ( name OH2  and z >-50 and z <35)"]
     
     cd
     cd Desktop
     $smd writepdb less_water.pdb



  - 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
  - Then upload to the CHARMM-GUI PDB reader
  - Be sure to keep certain options like the terminal group patching consistent
  - Be sure to preserve any disulfide bonds... check everything
  - On the appropriate screen select "rename" to rename the different components to the original names
  - Check that all the components are there after this step and download the contents
  - Upload the *.pdb, *.psf, *.crd, *.str, and copy the NAMD toppar folder from the original simulation and place in a new folder
  - Then follow the instructions on the NAMD 1D PMF to restart the simulation from a set of given *psf, *pdb ...
  - Edit the *.str to mimic many of the lines from the old simulation's *str since this *.str was written for CHARMM and we're using NAMD
  - 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
  - Delete the lines that correspond to the "# planar and Pulling restraints" that were used in the actual PMF, or adjust if needed



**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" 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
  - Continue through the steps to get the output and download it and pick up after the "rename" step in the steps above