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Example of MDFF

This page shows three representative examples to run MDFF:

Explanations:

Steps to run MDFF:
  1. 1. Generate the "*.psf", "*.dx", "*grid.pdb" and other files and assign the domain definition to the starting model using VMD based on the starting model and the cryo-EM density map (see MDFF tutorial )

  2. 2. The following command was used to run the MDFF domain rigid-body assembly:
      mdff setup -o domain -psf xxx.psf
         -pdb xxx.pdb
         -griddx xxx.dx
         -gridpdb xxx-grid.pdb
         -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
         -gscale 1.0
         -minsteps 2000
         -numsteps 200000

  3. 3. After the rigid-body assembly, the following command was employed to run the flexible refinement in the direct MDFF:
      mdff setup -o adk -psf xxx_autopsf.psf
         -pdb xxx_autopsf.pdb
         -griddx xxx_autopsf-grid.dx
         -gridpdb xxx_autopsf-grid.pdb
         -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
         -gscale 1.0
         -minsteps 2000
         -numsteps 500000
      mdff setup -o adk -psf xxx_autopsf.psf
         -pdb xxx_autopsf.pdb
         -griddx xxx_autopsf-grid.dx
         -gridpdb xxx_autopsf-grid.pdb
         -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
         -gscale 0.3
         -minsteps 2000
         -numsteps 500000
         -step 2
      mdff setup -o adk -psf xxx_autopsf.psf
         -pdb xxx_autopsf.pdb
         -griddx xxx_autopsf-grid.dx
         -gridpdb xxx_autopsf-grid.pdb
         -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
         -gscale 10
         -minsteps 2000
         -numsteps 0
         -step 3

    where "-numsteps" of the first two steps of the flexible fitting should set to 200000 in cMDFF (cases with map resolution < 5 Å).
NOTE:
  1. Please remember to run the domain rigid-body assembly and flexible refinement in order using the above commands. Otherwise, you may fail to run the MD simulation of MDFF.
  2. The domain definition should be assigned to the starting model "initial_model.pdb" before running the domain rigid-body assembly of MDFF. The method to assign the domain can be found in the MDFF tutorial.
  3. Please read README.txt if you download the tarball file of each case.