Error :Too many neighbors; overflow ignored:
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".)
Hi,
I solved my problem.
It was indeed correlated to the missing ATOMS present in the .ini file.
I realized the structural alignment program I used artificially added 'missing atoms' in my pdbs. Then it aligned all atoms during the alignement process generating an artificial deviation of the missing atoms from their 9999 value.
The resulting pdb couldn't be used by Modeller, most probably because the 'missing atoms' were not recognized as missing. I guess they were considered as atoms at 9998 angstrom (for instance) from the cell origin...
a bit too far, isn't it...
I am not sure this comment will be usefull to somebody else, but who knows...
Best,
David
Le 15 avr. 2015 à 19:14, Stroebel D a écrit :
> 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".) > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
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Stroebel D