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