Hi, I encounter this error too ... It works on my Debian Linux x86, but it fails on my Fedora Linux x86_64 .
I don't know why ..
Yun
On 2008年3月18日 星期二, Modeller Caretaker wrote: > Florian Odronitz wrote: > ... > > > 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. > > Ben Webb, Modeller Caretaker