Hello;
Is there a limit in the number of atoms when using the function "make a bond"? I was trying that in a polypeptide of 450 standard residues (I made it a single model) and it did not work.
Just to not be cryptic, that need arises from having modeled by special techniques the initial portion of the polypeptide. Now I would like to replace that portion with the modeled one. I had restrained with rmsd-colvars the dihedrals of a short stretch of alpha helix, so that I could align the modeled portion with the polypeptide.