example4

Example 4

Topology-only workflow: Generate topology files from an existing mixed crosslinked fibril PDB

Overview

This example demonstrates topology-only mode, where ColBuilder generates GROMACS topology files from an existing fibril PDB file without running sequence generation or geometry generation steps. This is useful when you:

• Already have a complete fibril structure
• Want to regenerate topology with different force field parameters
• Need to create topology for a fibril obtained from another source
• Want to switch between atomistic (amber99) and coarse-grained (martini3) representations

Workflow Summary

Input: Existing Mixed Fibril PDB
         ↓
   [Topology Generation Only]
         ↓
Output: Topology Files (.top, .itp, .gro)

Files and Usage

Input Files

• config_ex4.yaml
  → Configuration file for topology-only mode
  → Usage:

  colbuilder --config_file config_ex4.yaml

• collagen_fibril_rattus_norvegicus_MIX.pdb (provided by user)
  → Pre-existing fibril PDB file with mixed crosslinks
  → Can be from a previous ColBuilder run or any compatible source

Output Files

Main Topology Files

• rattus_norvegicus_topology_files/
  → Directory containing all topology files for GROMACS

• collagen_fibril_rattus_norvegicus.top
  → Main GROMACS topology file

• collagen_fibril_rattus_norvegicus.gro
  → GROMACS structure file with coordinates

Individual Model Topology Files

• col_0.itp, col_1.itp, ..., col_N.itp
  → Individual topology files for each collagen model in the fibril
  → Contains atom definitions, bonds, angles, dihedrals
  → Includes crosslink bonded terms (bonds, angles, dihedrals)

Important Notes

Automatic Connectivity Detection

In topology-only mode, ColBuilder:

• Automatically detects model connectivity from crosslink positions
• Identifies which models are connected through crosslinks
• Works with divalent (D), trivalent (T), or mixed (M) crosslink patterns
• Generates appropriate bonded terms for inter-molecular crosslinks

Force Field Options

You can generate topology files with either:

• force_field: "amber99" - All-atom representation
  → Best for detailed atomistic simulations
  → Larger system size, higher computational cost

• force_field: "martini3" - Coarse-grained representation
  → Suitable for longer timescales and larger systems
  → Reduced system size, lower computational cost
  → Requires Martinize2 installation

Switching Between Force Fields

To generate topology with a different force field:

1. Keep the same input PDB file
2. Change only the force_field parameter
3. Run ColBuilder again

Example for atomistic topology:

force_field: "amber99"

Example for coarse-grained topology:

force_field: "martini3"

Common Use Cases

1. Regenerate Topology After Manual Edits

If you manually edited a fibril PDB file and need new topology:

colbuilder --config_file config_ex4.yaml

2. Create Both Atomistic and Coarse-Grained Topologies

Generate amber99 topology:

# config_amber.yaml
force_field: "amber99"
# ... rest of config

Then generate martini3 topology:

# config_martini.yaml
force_field: "martini3"
# ... rest of config

colbuilder --config_file config_amber.yaml
colbuilder --config_file config_martini.yaml

3. Topology from External Source

If you obtained a collagen fibril PDB from another source:

1. Identify the crosslink types present
2. Make sure they are available in colbuilder database and set appropriate n_term_type, c_term_type and combinations
3. Run topology-only mode

Debug Mode

For troubleshooting, enable debug mode:

debug: true
topology_debug: true

This preserves:

• Intermediate topology files
• Temporary PDB files
• Detailed processing logs

References

• For crosslink types and combinations: crosslinks.csv
• For configuration details: Configuration Reference
• For topology generation: User Guide