Re: [modeller_usage] Adding glycans in AutoModel?

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

On 3/19/21 9:33 AM, Steven Truong wrote:
> I was hoping to ask if there is a way to automate glycan-building in 
> Modeller.  I’ve been able to get all residues/atoms built using 
> AutoModel.  However, I lose the glycan information when using AutoModel. 
>   Is there another program that interfaces well with Modeller, or is 
> there a class in Modeller that can add glycans at known positions (e.g. 
> if I know NAG is attached to residue 6, can I add that to the PDB output 
> somehow?).

To do this you would need to
1. Add residues for each sugar.
2. Add bonds between your glycoslyated residues and sugar residues, and 
perhaps also between sugars.

You would need a fairly good understanding of CHARMM topology files, 
including patch residues. See for example 
https://salilab.org/modeller/FAQ.html#8 and 
https://salilab.org/modeller/FAQ.html#9

There is no recipe out of the box to do this in Modeller, but AllosMod 
can do it. See https://modbase.compbio.ucsf.edu/allosmod/help.cgi?type=glyc

You are certainly welcome to use the AllosMod CHARMM topology file and 
the Python code it uses to generate AutoModel inputs. See 
https://github.com/salilab/allosmod-lib/blob/main/data/top_all_glyco.lib 
and 
https://github.com/salilab/allosmod-lib/blob/main/lib/allosmod/get_pm_glyc.py 
respectively.

	Ben Webb, Modeller Caretaker
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