Klauda Lab Simulation Wiki

Written By Robert

To Adjust the water level of the simulation (Robert):

1. Generate a PDB of the simulation using the steps from the NAMD PMF section where the PDB of the adjusted simulation is generated.
2. Download and open the PDB in VMD
3. 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

1. Find the edited PDB on the desktop
2. Need to include all the sections of the simulation including all the different proteins or peptides or drugs or any other missing molecules
3. Then upload to the CHARMM-GUI PDB reader
4. Be sure to keep certain options like the terminal group patching consistent
5. Be sure to preserve any disulfide bonds… check everything
6. On the appropriate screen select “rename” to rename the different components to the original names
7. Check that all the components are there after this step and download the contents
8. Upload the *.pdb, *.psf, *.crd, *.str, and copy the NAMD toppar folder from the original simulation and place in a new folder
9. Then follow the instructions on the NAMD 1D PMF to restart the simulation from a set of given *psf, *pdb …
10. 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
11. Use the Xmin and Xmax, Ymin… to get the lengths of the different axis
12. Update the number of waters now that it has been adjusted

To Mutate an Amino Acid (Mahdi)

1. Start with a PDB file of a given equilibrated simulation
2. Upload this PDB to CHARMM-GUI
3. Be sure to keep certain options like the terminal group patching consistent
4. Be sure to select “mutate” to mutate all the different residues, should be one of the first screens
5. Be sure to preserve any disulfide bonds… check everything
6. Select the “rename” option to essentially allow the various components to be recognized by the computer
7. Continue through the steps to get the output and download it and pick up after the “rename” step in the steps above