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#Pymol tutorial online code#

In Calculate Grid Center by Selection, write EFP. Plugin will not work, if you do not save.Ĭlick tab Grid settings. Working Directory: /home/you/another/pymol/workingdirĮnlarge the window and click Save Plugin Configuration file. Vina executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/autodock_vina_1_1_2_linux_x86/vina # Platform dependent

Check/set the executable to folders (they should be automatically found):Īutodock Tools: /home/you/another/pymol/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24Īutogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autogrid4 # Platform dependentĪutogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autodock4 # Platform dependent

#Pymol tutorial online code#

This code has been put under version control in the project Pymol-script-repo Note, that the module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them Create by: create ROC_A, 1HXB and resn ROC and alt a. Ligands can not be in alternative configuration.The Autodock tools, does not like funny atoms names like "C1, N13, O28" and so on.Watch Dan Seeliger's autodock plugin tutorial. This plugin is ready "out-of-box" for win users through the project Pymol-script-repo This plugin is ready "out-of-box" for Linux users through the project Pymol-script-repo Windows

Setup of a docking grid for Autodock with PyMOL.

This plugin should help to set up docking runs with Autodock and view docking results.

6 Example 2 - Alternative configurations of a Ligand.

5 Example 1 - Rename of funny atom names.