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PRELYM

File Preparation Guide
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Input File Preparation

To execute PRELYM, three input files are necessary. Choose between automated preparation or manual step-by-step process.

Choose Your Method
  • 🤖 Automated: Enter protein name or PDB ID - we'll prepare all files automatically
  • 📋 Manual: Follow the step-by-step guide below using web tools
  • Use pH 8.0 for consistency with experimental validation studies

🤖 Automated File Preparation

Let PRELYM automatically prepare your files by searching for proteins or downloading specific PDB structures.

Enter the protein name for database search
pH for protonation states
Force field for charge assignment
OR

📋 Manual Step-by-Step Guide

Follow these steps to manually prepare your files using external web tools:

Step 1: PDB Structure
Required: Clean PDB file
  1. Download your protein PDB file from RCSB PDB
  2. Open in Discovery Studio or similar molecular modeling software
  3. Remove all water molecules from the structure
  4. Add any missing atoms using the software's repair tools
  5. Save as a new PDB file with a descriptive name
Output: Clean PDB structure without water molecules
Step 2: H-bond Analysis
Required: PDB with optimized hydrogens
  1. Visit MolProbity web server
  2. Upload your clean PDB file from Step 1
  3. Use the "Add Hydrogens" functionality
  4. Allow the server to optimize hydrogen atom positions and bond lengths
  5. Download the hydrogen-complete PDB file
Output: PDB file with fully optimized hydrogen atoms
Step 3: Charge File
Required: PQR with partial charges
  1. Go to APBS server
  2. Select "PDB2PQR" job configuration tool
  3. Upload your clean PDB file from Step 1
  4. Set pH to 8.0 (or match your experimental conditions)
  5. Ensure "create an APBS input file" is checked
  6. Submit job and download the generated .pqr file
Output: PQR file with atomic partial charges
File Validation Checklist
PDB Structure File
  • Contains ATOM records
  • No water molecules (HOH)
  • Complete amino acid residues
  • Proper PDB format
H-bond Analysis File
  • Hydrogen atoms present
  • Optimized bond lengths
  • PDB format maintained
  • Same sequence as Step 1
Charge File
  • PQR format
  • Partial charges assigned
  • Correct pH settings
  • All atoms included
Example Files: Chymotrypsin
Download Example Files

We've provided pre-prepared Chymotrypsin files for testing PRELYM:

4CHA.pdb 4CHAFH.pdb 4CHA.pqr
Common Issues & Solutions

Solution: Use molecular modeling software (Discovery Studio, PyMOL, or ChimeraX) to add missing atoms. Ensure all backbone and sidechain atoms are present before proceeding.

Solution: Ensure your PDB file is clean and properly formatted. Try alternative tools like Reduce (part of Phenix suite) or ChimeraX's hydrogen addition feature.

Solution: Check for non-standard residues or missing atoms. Try different forcefield options (AMBER, CHARMM, PARSE) in PDB2PQR settings.