Does pmx support FEP calculation including carbohydrates (specifically NAG)?

[kva0987]

Hi,

I am currently stuck at the initial part of the process, where I am trying to pdb2gmx antibody-antigen complex that includes NAG on antigen (near epitope). I want to assess how different mutations can accommodate NAG better.

When I try to pdb2gmx my .pdb, I get an error saying that the forcefield do not have NAG in residue topology.
"Residue 'NAG' not found in residue topology database"

Is there a way to include NAG to the forcefield? Even if I did, would the calculated delta_G correctly reflect it?

I would appreciate any help.

Best,

[kva0987]

I think that there should be an easy way as it can incorporate DNA. Please give me any help.

[vgapsys]

It seems that this question is not directly related to pmx. If you want to simulate a non-canonical amino acid, you need its parameters to be added added to the protein force field. I suggest to explore how to parameterize amino acids and incorporate new block into the corresponding ff.