I've been working on the problem I posted earlier, in which Modeller
was removing the Calcium ions from my model, even though I put them in the
alignment file. I was able to reproduce the problem using a much smaller
file, and I found that I had to do two things to get the model to retain
the ions. One was to SET HETATM_IO = on in the .top file. I guess this was
mentioned somewhere in the archives, but it was certainly hard to find.
The other thing that seemed to be necessary was to put the heteroatom listing
in the source .pdb file as follows:
HETATM 542 CA CAL 71 -13.638 53.352 31.500 1.00 12.29
When I changed the name of the atom from CAL to CA, then it worked. But
the file it produced had converted this back again:
HETATM 538 CAL CAL 71 -9.629 53.605 27.498 1.00 67.12
I'm not sure what is going on here.
The log file still has a pair of errors:
delete__442E> One or more atoms absent from MODEL: O: 70: C: 70: N:
71: CA: 71:
delete__442E> One or more atoms absent from MODEL: O: 71: C: 71: N:
72: CA: 72:
The 2 ions are residue numbers 71 and 72, and it seems to be trying to find
amino acid backbones for them!
There are also a number of warnings in the log file, which can be seen by
looking in the .log file in the attached zipped archive. It seems to be producing
an adequate model now, but if anyone can tell me what is going on, I would
appreciate it.
John Penniston
Attachment:
Lobe.zip Description: Zip compressed data