my question has already been posted a couple of times - however these posts
date back a couple of years. That is why I hope to find new answers to this
topic.
The three options you quote are still the same...
I would prefer the third option and define them myself, but as the manual
states, this is a "painful" process.
Note also that Modeller generates restraints based on homology, and its
database contains many examples of TYR aligned with other standard
template residues, but none of phosphotyrosine, so you will get fewer
restraints on these residues.
I wonder if anyone has generated the needed files/entries for the modeler
libraries. There is a page in the Modeller Wiki that allows upload of these
customized files. It is empty however.
Since I currently do not have access to QUANTA or CHARMM, I cannot generate
the files myself.
The parameter and topology files are, however, just text files and you
can create them in any text editor. You may be able to find suitable
files at www.charmm.org; Modeller parameter/topology files are basically
the same as CHARMM files, just with some atom names modified to match
PDB naming.
I also wonder why the library file for residues in modeller 9v7 still dates
back to 1993?