Common applications of the MMTSB toolset

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Preparing protein simulations (from PDBfile to CHARMM trajectory):

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Preparing protein:DNA simulations (from PDBfile to CHARMM trajectory):

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Preparing protein simulations for replica-exchange:

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Visualizing the electrostatic surface potential of a macromolecule:

First, we select the protein from a PDB file (1enh.pdb), add hydrogen atoms, and center the molecule at the origin. Then, we calculate the electrostatic potential on a grid and generate the molecular surface of the protein. Finally, we view the molecule in VMD, projecting the electrostatic potential onto the molecular surface.

convpdb.pl -nsel protein 1ENH.pdb | complete.pl | convpdb.pl -center > 1enh.center.pdb
pbCHARMM.pl -emap phi.dx 1enh.center.pdb
pbCHARMM.pl -dx -grid epsx grid.dx 1enh.center.pdb
vmd 1enh.center.pdb phi.dx grid.dx

In vmd, select:
Graphics/Representations/Drawing Method [Surf]
Graphics/Representations/Coloring Method [Volume]

For a more thorough description, see the MMTSB Tool Set - Continuum electrostatics calculations tutorial.


For more examples, download and follow the tutorials prepared for past MMTSB workshops.