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:
(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
(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