On 5/18/12 1:20 AM, NUTAN CHAUHAN wrote: > I am trying to model a homodimer with heteroatoms from a homodimer > template. when make homodimer without heteroatoms it goes fine but when > i try to build homodimer with heteroatoms it doesn't run and shows some > errors regarding alignment mistakes.
OK, so the problem is your alignment doesn't match your PDB. You just need to fix that.
> What should be the alignment look like?
The alignment looks fine, but of course you didn't attach your PDB file so there's no way to independently tell whether they match. But the Modeller error message below looks pretty clear to me:
> Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH > PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE > Match ***** * * *
(The formatting got a little messed up in the email, but if you look in the original log file it should be lined up properly.) You have one more '.' in your alignment file in the B chain than you have in the PDB. Either you deleted one too many HETATM residues from your PDB file, or you added one too many to your alignment file.
Ben Webb, Modeller Caretaker