Avogadro Tutorial

This tutorial will guide you through building a peptide in Avogadro and preparing it for use in simulations, with attention to chirality editing for D-amino acids.

---

Step 1: Open Avogadro and Build Peptide

1. Launch Avogadro.

2. Navigate to the top menu: Build → Insert → Peptides

1. In the Insert Peptides window, click to add the desired amino acids to construct your peptide. Example: KYFIL → Lys-Tyr-Phe-Ile-Leu

---

Step 2: Modify to D-Stereochemistry (if needed)

For D-amino acids, you must manually invert chirality:

1. Deselect the entire structure: Select → Select None

1. Manually select the α-carbon on the amino acid residue (and β-carbon for Ile):

2. Only select the α-carbon and adjacent β-carbon for each D-amino acid.

1. Invert chirality: Build → Invert Chirality (or right-click if using tools)

Repeat for each D-residue. Avogadro does not automatically label chirality, so this step is crucial for accuracy.

---

Step 3: Save and Modify PDB File

After saving your .pdb file:

• For D-residues, manually update the residue names in a text editor:

• Change 3-letter amino acid codes to include a D prefix (e.g., TYR → DTYR).

• Ensure there are no spaces in the updated codes.

---

Step 4: Use CHARMM-GUI for Further Processing

1. Go to CHARMM-GUI PDB Reader.

2. Upload your edited PDB file under PDB Reader & Manipulator.

1. Leave the default settings unchanged.

1. Amidate the C-terminus by checking the appropriate box.

1. Download the processed files (e.g., PSF and PDB).

1. Open the downloaded .pdb file and reapply the D-prefix to any D-residues if CHARMM-GUI reverted them.

---

Notes

• For L-amino acids, you do not need to invert chirality or change residue codes.

• After generating your final structure, proceed to the appropriate tutorial:

• For atomistic simulations, use the NAMD or GROMACS workflow.

• For coarse-grained simulations, continue to the Coarse Grain with GROMACS Tutorial.

---