Glycosidic links in sugar chain not recognized by pdb2gmx

User discussions
1

Brief description of tools/files:
I am having a problem when trying to build from scratch the topology of a glycosylated protein. I created the system using CHARMMGUI, but I cannot create the simulation box due to the size of my system.

When giving the PDB file to pdb2gmx, using charmm36-jul2021.ff, it does not recognize the glycosidic bonds. Therefore, the program gives an error message that states that the O1 (linked to the next carbohydrate) of the carbohydrate is missing (see below). I was wondering if there’s a way to define this bond (definition in specbond.dat does not work) similar to the one implemented for the N-termini of proteins. So far, I have not found any tutorial to create a Charmm topology for a glycosylated protein from scratch. If one exists and you could redirect me to it, I’d appreciate it.

Thanks a lot for your help.

Program: gmx pdb2gmx, version 2020.6
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)

Fatal error:
Residue 262 named BGLC of a molecule in the input file was mapped
to an entry in the topology database, but the atom O1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

I don’t understand what this means. CHARMM-GUI should be able to do everything for you from start to finish in terms of construction.

GROMACS does not handle branched species like glycoproteins well. Its support for bonded structure like what is required here is minimal, and I would not attempt to build a complex glycoprotein in GROMACS at all, honestly. Use CHARMM-GUI, even if it is just for the initial construction of the solute coordinates and topology. Bypass pdb2gmx entirely here.