Error :Too many neighbors; overflow ignored: - modeller_usage

15 Apr 2015


      Hi,
I am currently building a model of a protein complex.
My models (automodel) were working fine. Trying to improved the input
(introducing missing atoms, chain breaks, new multitemplate...) I got
stuck with a log file finishing like this:
"
make_re_417_> Restraint type to be calculated:  phi-psi_binormal
Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:     20567746
 20085.689    19.615
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch1.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch1.mdt
neighs__292W> Too many neighbors; overflow ignored:       51       50
neighs__292W> Too many neighbors; overflow ignored:       51       50
"
...The last line being repeated as if it was the output of an infinite loop.
I guess my alignement and pdb are good because they have worked
previously and if any misalignment is present, the error messages should
appear before the ini file is created.
My .py has nothing special. (see at the end of this message.)
The program created the .ini, but not the .rsr file.
The .ini files looks ok unless for one thing: I was surprised that the
missing atoms in the file are still represented as 'missing' in the ini
output. example:
"ATOM  23557  CG  GLN J2975    9998.0019998.0019998.001  0.00 99.99
   C "
Shouldn't the remaining unknown coordinates having been rebuild using
internal coordinates from the Charmm topology library BEFORE the writing
of the ini file? (it may be an unrelated issue...)
(The Ini file also contains:
SSBOND lines at the beginning and
CONECT lines at the end)
I come to you since I didn't find anything usefull to explain this error.
If you have any idea where it could come from, I would be very gratefull
if you could share it!
Thanks in advance.
David
my.py
:
"
from modeller import *
from modeller.automodel import *    # Load the automodel class
from modeller import soap_protein_od
log.verbose()
# directories for input atom files
env = environ()
env.io.atom_files_directory = ['.','../atom_files']
class MyModel(automodel):
     def special_restraints(self, aln):
        rsr = self.restraints
        at = self.atoms
a = MyModel(env,
            alnfile  = 'AllAlignfinal.ali' ,          # alignment filename
knowns   = ('TMD', 'TMD2', 'TMD3', 'TMD4') ,    # codes of the
templates
            sequence = 'TMDRat' ,                     # code of the target
assess_methods = (assess.DOPE,
                              soap_protein_od.Scorer()
                                             ))
a.starting_model= 1                 # index of the first model
a.ending_model  = 3                 # index of the last model
                                    # (determines how many models to
calculate)
a.md_level = refine.fast
a.make()                            # do homology modelling
"
I let the "special restraints" definition because I may have to use it for
an other modelling step, but it has no use here. (and it is not involved
in my problem - tested)
Please note that I give you here a multi-template model building (on
multichain template), but adjusting the file to a single template gives
the same error message. The "soap library" is also (of course) not
involved (tested).
(Sorry, I first send this message to "modeller-care", but obviously it is more a problem of "usage".)