u/SeriousAudience

Hello, I need to do molecular dynamics simulation for several proteins with non-canonical, modified amino acid residues. For example: PDB IDs 1ATN and 1VIB in RCSB database. The modifications for protein residues can come from biologically post-translational modification (PTM) (phosphorylation, glycosylation, etc.) or artificially attaching small molecules via covalent bonds (such as fluorescent proteins). My questions are:

1. In principle, what are the steps to simulate modified residues? How to do force field parameterization for modified amino acids and integrate the force field for the modified residues with the force field of the canonical residues for the rest of the protein?
2. Does the method for force field parameterization differ between PTM or artificial attachment of small molecules?
3. I'm using OpenMM to simulate. Is there a well-established protocol to simulate modified residues within the OpenMM software ecosystem?

Thank you for reading my questions.

Hello, I need to do molecular dynamics simulation for several proteins with non-canonical, modified amino acid residues. For example: PDB IDs 1ATN and 1VIB in RCSB database. The modifications for protein residues can come from biologically post-translational modification (PTM) (phosphorylation, glycosylation, etc.) or artificially attaching small molecules via covalent bonds (such as fluorescent proteins). My questions are:

1. In principle, what are the steps to simulate modified residues? How to do force field parameterization for modified amino acids and integrate the force field for the modified residues with the force field of the canonical residues for the rest of the protein?

2. Does the method for force field parameterization differ between PTM or artificial attachment of small molecules?

3. I'm using OpenMM to simulate. Is there a well-established protocol to simulate modified residues within the OpenMM software ecosystem?

Thank you for reading my questions.