AMBER Archive (2009)
Subject: [AMBER] database
From: Steve Seibold (seibold_at_chemistry.msu.edu)
I am now trying to use the file.mol2 as a prepin file so that when I load my protein/ligand complex I can generate topology and inpcrd files. I am not sure how to go about this since the ligand.mol2 is not really a prepin file. I tried to use it as such but got "atom type" errors even though the atom names of my ligand.pdb and ligand.mol2 are equivalent. I then found in the AMBER8 manual the program "database" and thought my be this is what I can use to construct a prepi file from a mol2 file. However, it needs an atom definition file and I am not sure where to get this or what it really is. Is it the ligand.frcmod file I generated? Is there proper way of using mol2 files to generate topology and inpcrd files that I am missing? I looked on the AMBER web reflection site, but found no answers.