Please note that I used the dope_loopmodel class instead of loopmodel
as indicated in the manual.
When I run the script, it exits with the following message:
...
check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity).
The objective function can thus not be calculated.
Using dopehr_loopmodel gives the same error whereas the "old"
loopmodel works.
Here is the Atom record from the PDB file:
ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294
The coordinates do not seem to be out of range. I also put a blank in
the middle ("1.00 103.06") to avoid problems with the parser, but to
no avail.
The error refers to the current set of coordinates (during optimization)
- not the initial PDB coordinates. And don't put a blank into the PDB
file - PDB files are fixed-column format, so it doesn't matter that
there's no space between 1.00 and 103.06 (in fact, your "fixed" PDB file
is now invalid).
An atomic coordinate at infinity is usually a symptom of large forces in
your system. These can occur if you have a bad initial model (e.g. two
atoms superposed or very close). It is more likely to occur with DOPE
loop modeling than regular loop modeling since the former includes
GB/SA. (The loop modeling potentials themselves, while they are
atomistic pair potentials, plateau as r tends to 0, unlike electrostatic
potentials which tend to infinity.)
Am I doing something wrong here or is this a bug?
Could be either. You can try a different initial model if your initial
model is very bad. Otherwise, send me your input files and I'll try to
reproduce your problem, to determine whether it's a bug in the GB/SA code.