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Schrödinger Suite 2025-3

Version: 2025-3 Installation: /sw/schrodinger/2025-3 Module: schrodinger/2025-3 License: Commercial (Schrödinger License required)

Overview

The Schrödinger Suite is a comprehensive molecular modeling software package for drug discovery and materials science. It provides integrated tools for protein modeling, ligand design, molecular dynamics, quantum chemistry, and virtual screening.

Key Features: - Maestro graphical interface - Desmond molecular dynamics engine - Glide molecular docking - Prime homology modeling and protein structure prediction - Jaguar quantum chemistry - QikProp ADME prediction - FEP+ free energy calculations - BioLuminate antibody modeling - Materials Science Suite

Quick Start

Loading the Module

module load schrodinger/2025-3

Launching Maestro (GUI)

# Standard launch (software OpenGL)
maestro

# Hardware-accelerated graphics (if using VirtualGL)
vmaestro

# Direct command
$SCHRODINGER/maestro

# With specific license server
SCHROD_LICENSE_FILE=27008@license-server maestro

Main Applications

1. Maestro - Graphical Interface

maestro
  • Interactive molecular visualization and modeling
  • Workflow builder and job management
  • Structure preparation and analysis
  • Project management

2. Desmond - Molecular Dynamics

$SCHRODINGER/desmond input.msj -HOST localhost:4
  • High-performance MD simulations
  • GPU-accelerated
  • Protein-ligand binding
  • Membrane systems
  • Free energy calculations

3. Glide - Molecular Docking

$SCHRODINGER/glide input.in -HOST localhost
  • High-throughput virtual screening (HTVS)
  • Standard precision (SP) docking
  • Extra precision (XP) docking
  • Induced fit docking (IFD)

4. Prime - Protein Modeling

$SCHRODINGER/prime input.inp -HOST localhost
  • Homology modeling
  • Loop refinement
  • Side chain prediction
  • Protein-protein docking

5. Jaguar - Quantum Chemistry

$SCHRODINGER/jaguar run input.in -HOST localhost
  • DFT and ab initio calculations
  • pKa and tautomer predictions
  • Reaction mechanisms

6. QikProp - ADME Prediction

$SCHRODINGER/qikprop input.mae
  • Drug-like property prediction
  • ADME/Tox screening
  • Lipinski rule of five

Common Workflows

Protein Preparation

# Command-line protein preparation
$SCHRODINGER/utilities/prepwizard \
  -fillsidechains \
  -fillloops \
  -propka_pH 7.4 \
  -WAIT \
  input.pdb output.mae

In Maestro GUI: - Workflows → Protein Preparation Wizard - Preprocess structure - Review and modify structure - Refine structure (optimize H-bonds)

Molecular Docking with Glide

# Step 1: Generate receptor grid
$SCHRODINGER/glide receptor.in -WAIT

# Step 2: Run docking
$SCHRODINGER/glide dock.in -HOST localhost:4 -WAIT

Example grid generation input (receptor.in):

GRID_CENTER   25.0, 30.0, 15.0
INNERBOX      10, 10, 10
OUTERBOX      30, 30, 30
RECEP_FILE    protein_prepared.mae

Example docking input (dock.in):

GRIDFILE      receptor.zip
LIGANDFILE    ligands.mae
PRECISION     SP
DOCKING_METHOD confgen
POSES_PER_LIG  5

Molecular Dynamics with Desmond

# Create MD system
$SCHRODINGER/utilities/multisim \
  -m input.mae \
  -WAIT \
  -o output-md.cms \
  -set stage.set_family.md.jlaunch.in.file=desmond_md_job.msj

# Run MD simulation
$SCHRODINGER/desmond \
  -HOST "localhost:4:gpgpu=1" \
  -cfg desmond_md_job.cfg \
  -c desmond_md_job.msj \
  -WAIT \
  output-md.cms \
  -mode umbrella

Standard 100 ns MD workflow:

# Using Maestro workflow:
# 1. System Builder → Add membrane/solvent
# 2. Molecular Dynamics → Run Simulation
# 3. Simulation Interactions Diagram → Analyze

Virtual Screening

# High-throughput virtual screening
$SCHRODINGER/vsw \
  -SUBHOST localhost:20 \
  -glide-ligands library.mae \
  -glide-grid receptor.zip \
  -glide-precision HTVS \
  -glide-docking-method confgen \
  -WAIT

Free Energy Calculations (FEP+)

# FEP+ setup and run
$SCHRODINGER/fep_absolute_binding \
  protein.mae \
  ligands.mae \
  -WAIT \
  -HOST localhost:4:gpgpu=1

Homology Modeling with Prime

# Build homology model
$SCHRODINGER/prime_automatic_model \
  -seq target.fasta \
  -template template.pdb \
  -o model.mae \
  -WAIT

File Formats

Schrödinger uses several proprietary and standard formats:

Format Extension Description
Maestro .mae, .maegz Native Maestro format (compressed)
CMS .cms Chemical system (MD)
DMS .dms Desmond molecular system
PDB .pdb Protein Data Bank
SDF .sdf, .sd Structure Data File
MOL2 .mol2 Tripos MOL2
SMILES .smi Simplified molecular input
Grid .zip Glide receptor grid

Job Control and Hosts

HOST Specification

# Local host with 4 CPUs
-HOST localhost:4

# Local host with 4 CPUs and 1 GPU
-HOST "localhost:4:gpgpu=1"

# Multiple hosts
-HOST "localhost:8,compute-node:16"

# Slurm integration (via job scheduler)
-HOST "slurm:4:gpgpu=1"

Job Submission

# Submit job to run in background
$SCHRODINGER/jobcontrol -submit job.sh

# Check job status
$SCHRODINGER/jobcontrol -list

# Stop a job
$SCHRODINGER/jobcontrol -stop job_id

Environment Variables

Variable Purpose
SCHRODINGER Installation directory
SCHROD_LICENSE_FILE License server (format: port@server)
SCHRODINGER_TMPDIR Temporary directory for calculations
SCHRODINGER_HOSTS Default host configuration

Integration with Cluster

Batch Jobs via Slurm

Example Slurm submission script:

#!/bin/bash
#SBATCH --job-name=glide_dock
#SBATCH --cpus-per-task=8
#SBATCH --mem=16G
#SBATCH --time=24:00:00
#SBATCH --partition=general

module load schrodinger/2025-3

# Run Glide docking
$SCHRODINGER/glide dock.in \
  -HOST localhost:${SLURM_CPUS_PER_TASK} \
  -WAIT \
  -NJOBS 1

GPU Jobs

#!/bin/bash
#SBATCH --job-name=desmond_md
#SBATCH --cpus-per-task=4
#SBATCH --gres=gpu:1
#SBATCH --mem=32G
#SBATCH --time=48:00:00
#SBATCH --partition=gpu

module load schrodinger/2025-3
module load cuda/12.5

# Run Desmond MD with GPU acceleration
$SCHRODINGER/desmond \
  -HOST "localhost:${SLURM_CPUS_PER_TASK}:gpgpu=1" \
  -cfg desmond.cfg \
  -c desmond.msj \
  -WAIT \
  system.cms

Parallel Virtual Screening

#!/bin/bash
#SBATCH --job-name=vsw_screen
#SBATCH --cpus-per-task=32
#SBATCH --mem=64G
#SBATCH --time=72:00:00

module load schrodinger/2025-3

# Virtual screening with 32 parallel subjobs
$SCHRODINGER/vsw \
  -SUBHOST localhost:${SLURM_CPUS_PER_TASK} \
  -glide-ligands library.maegz \
  -glide-grid receptor.zip \
  -glide-precision SP \
  -WAIT

Python API (Schrödinger Python)

Schrödinger includes its own Python environment:

# Run Python script with Schrödinger modules
$SCHRODINGER/run python my_script.py

# Interactive Python shell
$SCHRODINGER/run python

# Install additional packages
$SCHRODINGER/run pip install package_name

Example Python script using Schrödinger API:

#!/usr/bin/env $SCHRODINGER/run python

from schrodinger.structure import StructureReader, StructureWriter

# Read structures
reader = StructureReader("input.mae")
for st in reader:
    # Process structure
    print(f"Structure: {st.title}, Atoms: {st.atom_total}")

# Write output
writer = StructureWriter("output.mae")
writer.append(st)
writer.close()

Utilities

Useful command-line utilities:

# Structure format conversion
$SCHRODINGER/utilities/structconvert input.pdb output.mae

# Split multi-structure file
$SCHRODINGER/utilities/maesubset input.mae -n 1-10 -o subset.mae

# Calculate molecular properties
$SCHRODINGER/utilities/ligprep \
  -isd input.sdf \
  -omae output.mae \
  -ph 7.0 \
  -pht 2.0 \
  -WAIT

# Prepare ligands
$SCHRODINGER/ligprep -isd ligands.sdf -omae ligands_prepared.mae -WAIT

Trajectory Analysis Tools

Schrödinger provides a comprehensive set of utilities for trajectory manipulation and analysis. These tools allow you to process, analyze, and modify molecular dynamics trajectories generated by Desmond.

See: Trajectory Utilities Reference

Common trajectory operations: - Alignment and centering: trj_align.py, trj_center.py - Format conversion: trj_convert.py, trj_merge.py, trj_slice.py - Analysis: trj_cluster.py, trj_essential_dynamics.py, trj_occupancy.py - Structure manipulation: trj_unwrap.py, trj_wrap.py, trj_parch.py - Subsystem extraction: trj_extract_subsystem.py

Quick example - align and center trajectory:

# Align trajectory to reference structure
$SCHRODINGER/run trj_align.py system.cms trajectory_trj aligned

# Center solute in simulation box
$SCHRODINGER/run trj_center.py system.cms centered -t trajectory_trj

For detailed documentation on all trajectory utilities, see the Trajectory Utilities Reference.

Documentation

  • Local Documentation: $SCHRODINGER/docs/Documentation.htm
  • Official Website: https://www.schrodinger.com/
  • Support Portal: https://www.schrodinger.com/support
  • Release Notes: $SCHRODINGER/docs/ReleaseNotes.html
  • Python API: $SCHRODINGER/docs/python_api/
  • Tutorials: $SCHRODINGER/docs/Tutorials/

Accessing Documentation

# Open main documentation in browser
firefox $SCHRODINGER/docs/Documentation.htm &

# List all documentation
ls $SCHRODINGER/docs/

# Python API documentation
firefox $SCHRODINGER/docs/python_api/index.html &

Tips and Best Practices

  1. Always Use -WAIT: Include -WAIT flag for command-line jobs to run synchronously
  2. GPU Acceleration: Use Desmond GPU version for MD (10-20x speedup)
  3. Protein Preparation: Always prepare proteins before docking or MD
  4. Save Projects: Use Maestro projects (.prj) to organize work
  5. Checkpoint Files: Desmond creates checkpoints for job recovery
  6. Memory Management: Large systems may require >32 GB RAM
  7. Tmp Space: Set SCHRODINGER_TMPDIR to fast local storage for performance
  8. Licenses: Check license availability before submitting many jobs

Troubleshooting

License Issues

# Check license status
$SCHRODINGER/licadmin STAT

# Test license connection
$SCHRODINGER/licutil -available

# Set license server explicitly
export SCHROD_LICENSE_FILE=27008@license-server

Graphics Problems

# Use software OpenGL (no GPU needed)
maestro -SGL

# Use VirtualGL for hardware acceleration
vmaestro

# Check OpenGL
glxinfo | grep "OpenGL version"

Job Failures

# Check job log files
tail job_name.log

# Monitor job progress
tail -f job_name.log

# Check host configuration
$SCHRODINGER/utilities/jserver -proxy -status

GPU Detection

# Test GPU availability
$SCHRODINGER/run gpu_info.py

# Check CUDA
nvidia-smi
module load cuda/12.5

Memory Issues

  • Increase job memory allocation: -JOBNAME job_name -maxjob 1 -maxsub 1
  • Set tmp directory to larger partition: export SCHRODINGER_TMPDIR=/scratch
  • Reduce system size or simulation complexity

Common Applications by Research Area

Drug Discovery

  • Hit Identification: Glide HTVS, Phase pharmacophore screening
  • Lead Optimization: Glide XP docking, Prime MM-GBSA, FEP+
  • ADME Prediction: QikProp, pKa predictions
  • Binding Analysis: Desmond MD, Simulation Interactions Diagram

Protein Engineering

  • Homology Modeling: Prime
  • Loop Refinement: Prime loop refinement
  • Protein-Protein: Prime PIPER docking
  • Antibody Modeling: BioLuminate

Materials Science

  • Polymer Modeling: Materials Science Suite
  • Surface Interactions: Desmond MD
  • Electronic Properties: Jaguar quantum chemistry

Example Workflows

Complete Protein-Ligand Study

# 1. Prepare protein
$SCHRODINGER/utilities/prepwizard \
  -fillsidechains -propka_pH 7.4 -WAIT \
  protein.pdb protein_prep.mae

# 2. Prepare ligands
$SCHRODINGER/ligprep \
  -isd ligands.sdf -omae ligands_prep.mae -WAIT

# 3. Generate receptor grid
$SCHRODINGER/glide receptor.in -WAIT

# 4. Dock ligands
$SCHRODINGER/glide dock.in -HOST localhost:8 -WAIT

# 5. Run MD on top complex
$SCHRODINGER/multisim \
  -m top_pose.mae -HOST "localhost:4:gpgpu=1" \
  -WAIT -maxjob 0 -o md_system.cms

# 6. Analyze MD trajectory
$SCHRODINGER/run simulations_analysis.py trajectory.xtc

Support

For technical support and questions: - Schrödinger Support: https://www.schrodinger.com/support - Knowledge Base: https://www.schrodinger.com/kb - User Forums: https://www.schrodinger.com/forum - Cluster Admin: Contact cluster administrators for module-specific issues

  • moe/2024 - Alternative molecular modeling suite
  • vmd/2.0 - Molecular visualization and trajectory analysis
  • gromacs/2025.0 - Open-source molecular dynamics
  • amber/24 - Amber molecular dynamics
  • cuda/12.5 - GPU acceleration for Desmond

Sample Data and Tutorials

# Sample data location
ls $SCHRODINGER/samples/

# Tutorial files
ls $SCHRODINGER/docs/Tutorials/

# Example scripts
ls $SCHRODINGER/mmshare-*/python/scripts/

Last Updated: October 2025 Module Maintainer: XLence Cluster Administration