Date: Wed, 26 Aug 2009 22:02:21 +0100
Dear Yikan,
I have a question: Does the TMS residue that you mentioned in your e-
mail consist of the HETATOM entries in your PDB? If I am looking at
it right, the PDB contains a nucleic acid, and it should be one large,
covalently-bonded molecule, correct?
Remember, antechamber can handle only one species (covalently bonded
molecule) at a time. If your TMS residue should be part of the
nucleic acid, why are they listed as HETATOM? I don't know whether
antechamber distinguishes between ATOM and HETATOM entries in a PDB
(the way CDCC Mercury does, see attached PNG file), but I think this
is a bit confusing. Probably a result of the software used to
generate the PDB.
The other issue is that your PDB file lists two MODELS, with very
similar coordinates (see lines that contain "MODEL 1" and
"MODEL 2"). Maybe you could try cleaning up this PDB file, and
then sending it to antechamber?
Good luck!
Nick Musolino
(image/png attachment: Picture_1.png)
- text/plain attachment: ATT00003.txt
- text/plain attachment: ATT00004.txt
