Hi,
Derek Smith wrote: > > Dear Tony and Antonello, > > I too had the problem of not getting heteroatoms in my models when I had > specified HETATM_IO = on. I sorted it out as follows... > > 1. Is the HETATM already parameterised in MODELER? > > if so... >
I had the same problem but with modified amino acid residues forming a chromophore. Here's my solution.
For simple model building, say the first round with a hetero residue or just an undefined residue, set these residue types to BLK in the pdb file and then indicate the positions by . in the alignment both in the known and unknown sequences. Even if these residues start with ATOM headers, Modeller is able to copy the coordinates over and rename them HETATM.
For each non-standard residue use a . and for a small molecule use /. to indicate that there is no covalent link between the protein and the BLK residue.
Rename the BLK residues back to their original names and if you had ATOM headers instead of HETATM, change these back as well in the output.
Good luck!
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