Hello everybody,
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.
Modeller (9v7) does not recognize phosphotyrosine residues (Phosporylated tyrosines, PTR). There are three options to deal with such undefined residues:
1. Use Tyrosine instead (and optionally after modelling: replace with phosphotyrosine und minimize) This might be a good choice, if the residues were in areas far away from the region under investigation
2. Use Block Residue (rigid body) - not the most accurate way, but a good workaround (http://salilab.org/modeller/9v7/manual/node95.html)
3. Define the unknown residue according to the manual/FAQ (http://salilab.org/modeller/FAQ.html#8)
I would prefer the third option and define them myself, but as the manual states, this is a "painful" process. 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. I also wonder why the library file for residues in modeller 9v7 still dates back to 1993?
I hope someone can help. Thank you in advance,
Cheers
Jan H. Loehr University of Hamburg, Germany