On 5/20/19 12:07 PM, Chakraborty, Srirupa via modeller_usage wrote: > I am trying to use allosmod package in MODELLER for ab initio modeling > of glycans
allosmod isn't part of Modeller, but it does use Modeller as one of its dependencies. See the AllosMod docs at https://allosmod.readthedocs.io/en/latest/ for more details. You can also dig through all the source code at GitHub to see exactly what is going on: https://github.com/salilab/allosmod-lib/
> (1) In the glycan modeling methods section of the paper, it is mentioned > that "initial structures were generated by addition of glycan chains > with ideal geometries derived from CHARMM, followed by a 1angstrom > randomization of the full atomic coordinates". I am assuming this > randomization is the same as the randomize_xyz function of MODELLER. > However, since templates are not being provided by the user for the > glycans, how are the sugar ring puckerings and dihedral angles correctly > reproduced even after such large random deviations?
AllosMod adds suitable restraints for each sugar residue using the CHARMM forcefield, as per https://salilab.org/modeller/FAQ.html#8. See top_all_glyco.lib and par_all_glyco.lib at https://github.com/salilab/allosmod-lib/tree/master/data.
> (2) My understanding is, in MODELLER, the solvation information is taken > implicitly from the template provided. However, since the glycans are > modeled template-free, is there any explicit treatment of solvation
No.
Ben Webb, Modeller Caretaker