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