AMBER Archive (2009)

Subject: [AMBER] database

From: Steve Seibold (
Date: Wed Sep 16 2009 - 09:59:14 CDT

Hello Amber
I have a mol2 file of a ligand which I have used to generate (using parmchk) a ligand.frcmod file. So, I have the ligand.mol2 and the ligand.frcmod. I changed the atom names of the ligand in my protein/ligand complex pdb file so that the names are equivalent to those found in the ligand.mol2 file.

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.

Thanks, Steve

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