on fish cluster, type sourceinsi, sourceindy, or sourceo2

then type insightII

----------------------

click on the top-left msi icon for module builder

under fragment click on get and pull up the fragment library of choice

here, click on Ala

to make Ala-trifluoromethylketone,

click on atom - replace to place a C atom where the carboxly linkage was found

to add H atoms, click on modify - hydrogens

to refine the geometry of the compound, click on optimize

to save the coordinates (say, in the PDB format), click on file - export

choose the PDB file type

 

in the Mol File Name box, give the name of the file to be saved (F3Ala.pdb)

and hit execute

to quit, click on session - quit