CHARMM Development Project
Posted By: Noah Force Field for Glycoproteins - 09/23/21 02:05 PM
Where can I find the files for force fields that are compatible with glycoproteins?

I initially thought CHARMM36 would be compatible. However, after I obtained by glycoprotein structure using CHARMM-GUI Glycan Modeler and tried running molecular dynamics simulation with it on GROMACS, the CHARMM36 force field was unable to recognize the glycan chain that I added.

Any help is appreciated. Thank you!
Posted By: rmv Re: Force Field for Glycoproteins - 09/23/21 03:23 PM
GROMACS does not read the CHARMM36 force field files natively; a conversion process is required.

It isn't clear if this is a charmm-gui problem, a problem with the force field conversion, or a user error.

The MacKerell site has a GROMACS conversion of CHARMM36 available.

(Note: your duplicate post has been deleted; see READ BEFORE POSTING topic.)
Posted By: Noah Re: Force Field for Glycoproteins - 09/23/21 07:25 PM
Sorry about the duplication, and thank you for the reply!

And yes, I was using the GROMACS conversion of CHARMM36, so I don't think that was the issue. Do you possibly know if CHARMM36 is supposed to support glycoproteins? If so, then I'll know that the problem I'm facing isn't due to the force field I'm using.
Posted By: rmv Re: Force Field for Glycoproteins - 09/23/21 09:15 PM
Absolutely; the CHARMM-GUI people (Wonpil Im et al) have used it to model the SARS-CoV2 spike protein, with all of its glycosylation; the citation is on their site.
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