Dear Ben,

I modified both the top.lib and restyp.lib in modlib fold to include the hydroxyproline information. The command line added to the restyp.lib is like this:

HETATM | HYP                 | O |   | HYP  | hydroxyproline

There are HYP residues indicated as HETATM in the template pdb file, and when I used a target sequence does not include O in the .ali file, I got the backbone.

However, when I used a target sequence containing O in the .ali file, I got the following error:

Then, I searched the archive: http://salilab.org/archives/modeller_usage/2010/msg00413.html

There, you said Modeller cannot build models containing modified amino acids.

If this is the case, how can  modifying both the top.lib and restyp.lib to add the nonstandard amino acids information make any sense?

Thanks in advance.