Re: CCL:Date: Wed, 16 May 2001 13:47:15 +0200

From: Bill Ross <>
Date: Wed 16 May 2001 12:59:11 -0700 (PDT)

        I'm new at AMBER and I try to learning it.
        Since I have always used TRIPOS I have lots of stuff in
        mol2 format I'd like to use in amber. ... but at the time I
        convert the mol2 molecules into PDB files all the problems come out.
        When I try to use the new PDB file, leap (or xleap) turned out that the
        molecule have no atom type.
        I checked and this is true, but I work with ligand-receptor
        complexes and unfortunately the ligands are not protein based
        molecules and are thus converted in a UNK residue.

You will need to make residue definitions for your ligands.
I advise looking at the streptavidin-biotin tutorial on the
amber web.

        I founf a tripos_util command, but it is
        not working or I do not how to use it.

If you can convert to pdb I don't think it will be necessary;
it has not been compiled or used by anyone still on the amber

Bill Ross
Received on Wed May 16 2001 - 12:59:11 PDT
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