Hi Jul,
Instead of making one, you could download a component cif file from the corresponding PDB entry for CGU:
https://www.rcsb.org/ligand/CGU
If your residue is embedded (linking two other residues through the backbone), you might have to make your own mainchain file. Tutorial 5 Section 3 does a great demonstration for that:
https://ambermd.org/tutorials/basic/tutorial5/index.php
If you need to modify the protonation state, you could edit the composition and specify the total charge of the residue to your liking, also in the mainchain file.
From: Kavinda Kashi Juliyan Gunasinghe via AMBER <amber.ambermd.org>
Date: Saturday, June 8, 2024 at 10:19 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Parameterization Issue
Dear AMBER users,
I have modelled an AF3 protein strucutre which consists of Gamma-carboxylated Glus (CGU). However, I have an issue with generating the Main Chain file for the which gives me several errors that in which several bond and angle parameters are missing. Can I know how I can generate the correct CIF file and then generate the correct main chain file for this protein? I have attached my protein structure in this email.
Thank you inadvance!
Jul
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Received on Sun Jun 09 2024 - 01:00:02 PDT
