ERROR IN MODELS ASSESSMENT
Dear All,
This is to inform you that I have introduced new residue type called BGC which has a Glycosidic linkage between ASP and Beta-D-GLUCOSE as mentioned in the following protocol https://salilab.org/modeller/6v2/FAQ.html#2. I can access this newly introduced residue successfully throughout the modeling but after the models generation I get the following warning message for the single models assessment.
>> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: BGC:N BGC iatmcls_286W> MODEL atom not classified: BGC:CA BGC iatmcls_286W> MODEL atom not classified: BGC:CB BGC iatmcls_286W> MODEL atom not classified: BGC:CG BGC iatmcls_286W> MODEL atom not classified: BGC:OD1 BGC iatmcls_286W> MODEL atom not classified: BGC:OD2 BGC iatmcls_286W> MODEL atom not classified: BGC:C BGC iatmcls_286W> MODEL atom not classified: BGC:O BGC iatmcls_286W> MODEL atom not classified: BGC:C1 BGC iatmcls_286W> MODEL atom not classified: BGC:O5 BGC iatmcls_286W> MODEL atom not classified: BGC:C5 BGC iatmcls_286W> MODEL atom not classified: BGC:C2 BGC iatmcls_286W> MODEL atom not classified: BGC:O2 BGC iatmcls_286W> MODEL atom not classified: BGC:C3 BGC iatmcls_286W> MODEL atom not classified: BGC:O3 BGC iatmcls_286W> MODEL atom not classified: BGC:C4 BGC iatmcls_286W> MODEL atom not classified: BGC:O4 BGC iatmcls_286W> MODEL atom not classified: BGC:C6 BGC iatmcls_286W> MODEL atom not classified: BGC:O6 BGC iatmcls_286W> MODEL atom not classified: ALA:OXT ALA preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append().
Here, I just want to know what does these statements implies "No fixed restraints selected; there may be some dynamic ones. Restraints file was probably not read; use restraints.append()"
Even, I added all these "BGC" atoms in "/atmcls-mf.lib" file but still I am getting this warning. So, Kindly let me know that is it necessary to worry about this warning ? If not can you guide me how to append this "BGG new residue" restraints?
Thanking you
On 12/12/16 5:10 AM, Mahesh Velusamy wrote: > This is to inform you that I have introduced new residue type called BGC > which has a Glycosidic linkage between ASP and Beta-D-GLUCOSE as mentioned > in the following protocol https://salilab.org/modeller/6v2/FAQ.html#2. I > can access this newly introduced residue successfully throughout the > modeling but after the models generation I get the following warning > message for the single models assessment. > >>> Model assessment by DOPE potential > iatmcls_286W> MODEL atom not classified: BGC:N BGC
DOPE is a statistical potential, so it's trained on known protein structures. Obviously we didn't include any of your BGC residues in the training set, so you should expect to see such a warning.
> preppdf_453W> No fixed restraints selected; there may be some dynamic ones. > preppdf_454W> Restraints file was probably not read; use restraints.append(). > > Here, I just want to know what does these statements implies "No fixed > restraints selected; there may be some dynamic ones. Restraints file was > probably not read; use restraints.append()"
These look fine too. Usually when you evaluate the scoring function you have at least some static restraints, such as stereochemistry, so Modeller will warn you if you try to evaluate the score without any static restraints. But DOPE consists entirely of dynamic restraints, so no problem here.
Ben Webb, Modeller Caretaker
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Mahesh Velusamy -
Modeller Caretaker