I’m trying to model a protein with a cyanocobalamin cofactor. I have
included CHARMM topology and parameter files using the corresponding
.append commands, created a custom residue for the cyanocobalamin in
restyp.lib and added atomic radii. Looks like there is a limit on the
number of atoms per residue… How can I increase this limit?
Sorry, you can't - the limit of 100 atoms per residue is hard-coded into
Modeller. (Even if you could, there are other limits that you'd run
into, such as a maximum number of bonds per residue.) If your cofactor
is present in the template, then you should be able to use a simple
block residue ('.' one letter code in your alignment) to copy it rigidly
from template to target instead - that shouldn't care how many atoms
there are. Or you could strip out the hydrogens - that should get your
atom count under 100. Or you could split the cofactor into several
residues, each with less than 100 atoms, and add suitable inter-residue
bonds (ugly, but it should work just fine).
I can look into removing this limit in future versions of Modeller. Can
you send me your topology file so I can make sure it works?