Hi,A couple of days before I started to use Screen, I made a pharmacophore using other program, but this program only make the pharmacopher not the screening of a database.I try to use the ScreenMD for perform the screening of a databae (NCI) using my pharmacophore (in .mol2 file) but it doesn't work. I use the JChem 5.1.04 windows.
screenmd can perform a database search using pharmacophore fingerprints that need to be generated prior to the searching. You can use a mol2 file to provide one or more query molecules, however, an explicit pharmacophore model cannot be passed to screen. It does build it's own hidden internal model from your queries (i.e. known actives).
The related user manual should help clarify the usage of these tools. Also, there is a tutorial in your JChem installation folder: examples\screen\index.html. That is a very useful and practical introduction to screen.