Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
courses:public:vmd [2016/06/21 09:29] stank [Visualization of electrostatic potentials] |
courses:public:vmd [2016/06/21 09:42] stank [Visualization of electrostatic potentials] |
||
|---|---|---|---|
| Line 147: | Line 147: | ||
| * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). | * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). | ||
| The proteins should show up as aligned entities. | The proteins should show up as aligned entities. | ||
| - | * Go to the PDB2PQR webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/ | + | * Go to the PDB2PQR webserver: [[http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/]] |
| * Upload one of the aligned coordinate files. | * Upload one of the aligned coordinate files. | ||
| Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | ||
| Line 172: | Line 172: | ||
| {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | ||
| - | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualizationstate alignment and electrostatics}} | + | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}} |
