Hello John,
You can include covalently modified residues in your sequence prior to the model building: i.e. you need to edit your seq alignment.
For the current list of residue types (about 30 "active" and 140 defined) please consult the $MODINSTALL6v2/modlib/retyp.lib file.
More details about it and about defining new residues: http://salilab.org/modeller/manual/node29.html
questions: 17, 18
best wishes, Andras
J Simms wrote: > > Hi All, > I have just started modelling a G Protein-Coupled Receptor, > which has a number of post translational modifications. My > problem is that my template, Rhodopsin, is glycosylated on the > extracellular loops at a different position to my target sequence. > Is there a way of adding the glycosylation to my target protein > either at the alignment stage or before the model in refined. > As always many thanks in advance. > > John.