Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?

EidRashed
Tue, 04 Nov 2025 09:35:30 +0000
pmx

Hi all,

I’d like to use PMX to compute ΔΔG of binding for an Fc that is N-glycosylated (structure based on PDB: 3WJJ) by reversing the mutation P238D. I know PMX supports Amber and CHARMM family protein force fields out of the box, but I’m unclear how best to proceed when linked glycans are present.

Concretely:

Amber/GLYCAM → GROMACS → PMX?
If I build the glycoprotein in tleap with Amber+GLYCAM, then convert to GROMACS formats (e.g., via ACPYPE or similar), is that topology/coordinate set acceptable input for pmx mutate? Key requirement: the covalent N-glycosidic bond (Asn–GlcNAc) must survive the conversion and be represented as a bonded connection in GROMACS. Has anyone run PMX successfully on such converted glycoprotein systems? (Background: GLYCAM→GROMACS conversion with ACPYPE is documented, but I’m not sure about PMX compatibility and preserving cross-residue bonds. )

All-CHARMM36 route with pdb2gmx + PMX CHARMM-mut ff?
Alternatively, prepare the glycoprotein entirely with CHARMM36 (jul2022) carbohydrate parameters in GROMACS (i.e., using carb.rtp/carb.r2b so mid-chain vs terminal sugar names map correctly), then use PMX’s CHARMM mutate workflow. Is there a recommended recipe (naming, r2b mappings for mid-chain GlcNAc, Man, Gal, Fuc, specbond.dat for linkages, etc.) known to work end-to-end with PMX? (GROMACS handles CHARMM36 glycans via carb.rtp + carb.r2b; correct residue naming and r2b mapping are critical. )

Any proven alternatives?
If the above aren’t practical, are there known workarounds (e.g., splitting protein/glycans, then merging with manual bonds in topology; or specific PMX mapping files for common N-glycans) that people have used successfully for ΔΔG with glycoproteins?

Motivation / constraints:
We prefer to avoid web services that require uploading proprietary coordinates (e.g., CHARMM-GUI), and we’re fine with some manual editing if that’s the current state-of-the-art. (We know CHARMM-GUI’s Glycan Reader/Modeler can produce GROMACS-ready glycoproteins; just checking for an offline/PMX-friendly path. )

Any pointers, example repos, or do/don’t tips (especially around PMX’s mutate step with carbohydrate-bearing topologies) would be hugely appreciated!

Thanks!

6 posts - 2 participants