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Difference between revisions of "Common applications of the MMTSB toolset"
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==Visualizing the electrostatic surface potential of a macromolecule:== | ==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. | |
| − | + | <small> | |
| − | <br> | + | <br><br>convpdb.pl -nsel protein 1ENH.pdb | complete.pl | convpdb.pl -center > 1enh.center.pdb |
| + | <br>pbCHARMM.pl -emap phi.dx 1enh.center.pdb | ||
| + | <br>pbCHARMM.pl -dx -grid epsx grid.dx 1enh.center.pdb | ||
| + | <br>vmd 1enh.center.pdb phi.dx grid.dx | ||
| + | <br><br> | ||
| + | </small> | ||
| + | In vmd, select: | ||
| + | <small> | ||
| + | <br>Graphics/Representations/Drawing Method [Surf] | ||
| + | <br>Graphics/Representations/Coloring Method [Volume] | ||
| + | </small><br><br> | ||
| + | For a more thorough description, see the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/MMTSB_PBCalculations/MMTSBPBCalculations.html MMTSB Tool Set - Continuum electrostatics calculations tutorial]. | ||
| + | <br><br><br> | ||
<b>For more examples,</b> download and follow the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html tutorials] prepared for past MMTSB workshops. | <b>For more examples,</b> download and follow the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html tutorials] prepared for past MMTSB workshops. | ||
Revision as of 14:56, 9 July 2009
Page currently under construction!!!
Contents
Preparing protein simulations (from PDBfile to CHARMM trajectory):
replace text
Preparing protein:DNA simulations (from PDBfile to CHARMM trajectory):
replace text
Preparing protein simulations for replica-exchange:
replace text
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.