On Tue, May 19, 2009, moitrayee.mbu.iisc.ernet.in wrote:
> Thanks a lot for the mail. I have already renamed the atoms in the pdb file
> 1QF6_TSB.pdb according to the atom names in TSB.in. The previous error showed
> after these modifications. I am attaching the pdb and prepi files.
> It would be great if you please suggest what might be the problem.
You pdb file doesn't give all of the TSB atoms the same residue number:
...
ATOM 13068 C14 TSB A2002 36.902 77.357 48.490 1.00 11.51
ATOM 13069 N6 TSB A2002 34.178 75.035 49.798 1.00 11.95
ATOM 13070 C12 TSB A2002 35.226 75.511 48.919 1.00 11.94
ATOM 13071 C13 TSB A2002 36.006 76.687 49.542 1.00 11.60
ATOM 13072 O9 TSB A2002 35.092 77.677 50.036 1.00 11.90
ATOM 13073 C11 TSB A2002 36.162 74.359 48.709 1.00 12.30
ATOM 13074 O8 TSB A2002 36.002 74.001 49.999 1.00 12.85
ATOM 6829 P1 TSB A1002 37.529 72.382 47.370 1.00 38.54 P
ATOM 6830 O6 TSB A1002 37.295 70.912 47.274 1.00 38.04 O
ATOM 6831 O7 TSB A1002 37.157 73.261 46.244 1.00 39.13 O
ATOM 6832 O3 TSB A1002 36.811 72.878 48.694 1.00 37.08 O
ATOM 6833 O2 TSB A1002 39.069 72.659 47.633 1.00 40.09 O
ATOM 6834 C10 TSB A1002 39.578 74.002 47.702 1.00 40.09 C
Note that the first 7 atoms have a different residue number than the atoms
that follow. Leap is confused into thinking that there are two residues here.
You need to fix up the pdb file so that the TSB residue all looks like it has
the same residue number.
[Aside: how to find something like this yourself: try to load just the TSB
part of the pdb file, e.g. with "x = loadpdb TSB.pdb". Then use the "desc"
command, e.g. "desc x.1". You will see two residues where there should only
be one. Breaking a pdb file into smaller pieces and using the desc command is
a common debugging strategy.]
...dac
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Received on Wed May 20 2009 - 17:30:06 PDT
