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...
2. Have you specified the HETATM in the alignment file? I use MODELER through QUANTA, which puts heteroatoms into the PDB input files but doesn't automatically put heteroatoms into the sequence alignment, so I have to edit the file manually.
3. Have you aligned the HETATMs for template and model sequence? If the hetatm for template and model sequence are not equivalent then your hetatm occurs in the postion of what would be the next C-alpha atom in your chain.
It's very basic I know - but sometimes mistakes can happen.
I hope it works out for you both.
Derek.
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!
Shoba ======================================================================= Shoba Ranganathan, Ph D Tel:+61-2-9351-1870 ANGIS, Bay 16, Suite 104 Toll free:1-800-728-028 Australian Technology Park Fax:+61-2-9351-1878 Eveleigh NSW 1430 Australia Personal URL: http://seal.angis.org.au/~shoba ================MolMod Home Page: http://molmod.angis.org.au===========
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Derek Smith -
Shoba Ranganathan