Re: [modeller_usage] Solvation and randomization in ALLOSMOD glycan modeling

[Modeller Caretaker <>]

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
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