Re: [modeller_usage] MAPRES limit

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 2/14/12 12:51 PM, Johs, Alexander wrote:
> 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?

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage