Protein
IQ
New batch
Loading batch setup…
Tool
Name
Project
Inputs
Protein
IQ
Home
Results
Library
Files
Collections
Projects
Visualize
PDB Viewer
MSA Viewer
Molecule Drawer
Playground
Tools
Batches
Workflows
AI Assistant
Management
Usage
Billing
API Keys
Team Members
Get free credits
Share or give feedback
New batch
Batch setup
Tool
PDB2PQR
Name
Project
No project
Inputs
Template
CSV / Excel
Paste CSV
Still loading the input checks for this tool. Try again in a moment.
Report an issue
Biomolecular structure
Upload files
or drag and drop
PDB, ENT, CIF, MMCIF · up to 50 MB
Ligand MOL2
Force field & Protonation
Force field
PARSE (default)
Use PROPKA for protonation
Structure options
Remove water molecules
Keep chain IDs
Clean only (no optimization)
Neutral N-terminus
Neutral C-terminus
Advanced settings
Debump structure
Optimize hydrogens
Assign charges only
Output naming scheme
Canonical naming (default)
Include original header
Whitespace-delimited PQR
Generate PDB output
Generate APBS input
Run APBS electrostatics
0 credits
0 jobs will be created.
Preview
Reset
Sign in to run