How to dock a database of peptides.

[Andrew Orry]

Question:

How can I dock a database of peptides using the Docking menu?

Answer:

• Setup a docking project as you do for small molecules: http://www.molsoft.com/gui/start-dock.html#docking-start
• Build your peptides in this text format .se as described here: http://www.molsoft.com/man/files.html#icm.se
• Use _dockScan DOCKING_PROJECT_NAME pept.se  (_dockScan is described here: http://www.molsoft.com/man/ligand-fit.html#dockScan)

[Andrew Orry]

There is a small error in the syntax on the _dockScan command in the original e mail below:

the line should read input=pept.se

e.g.

/icm/3.8-7c/icm64 /icm/3.8-7c/_dockScan mydock input=pept.se