User-friendly, easy-to-learn computational chemistry suite designed by chemists for chemists

SCIGRESS

Overview

SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.

A suite of molecular builders and visualization tools enable the researcher to build novel structures in minutes. Calculations of various chemical and physical properties are possible, as well as reaction modeling on various theory levels without the hassle of learning computational chemistry jargon.

Speed of and ease of simulations make on-the-fly testing of research ideas possible, before going to the wet lab in areas of organic, medicinal and biochemistry – saving time, money and reagents wasted on failed experiments.

Integrated, intuitive, property oriented GUI for building molecules and larger systems:
- Automated 2D -> 3D conversion with hydrogen addition.
- Library of popular organic molecules.
- Protein editor / peptide builder.
- Crystal builder.
- Builders for Molecular Dynamics systems (Solid state, liquid, amorphous, polymer, liquid crystal and more).

Fully automated process of job submission and data retrieval and analysis:
- Local and remote calculations run at a press of a button.
- Multi-step simulations.
- Chemical Spreadsheet for batch jobs and fully automated QSAR analysis.
Project explorer for tracking relations between input and output files.
Graphical representation of computed properties:
- Molecular editor/visualizer with highly customizable rendering options.
- Interactive spectra.
- Interactive potential energy graphs.
- Orbital and other electronic structural features visualization.
- Stereoscopic 3D visualization on compatible hardware.
Set of easily customizable predefined procedures for common calculations.
Seamless interface to external compute engines, both free and commercial:
- Amsterdam Modeling Suite.
- AutoDock (Tools and Vina).
- CONFLEX.
- GAMESS.
- Gaussian.
- LAMMPS.
- MOPAC.
- Quantum ESPRESSO.

Molecular Mechanics:
- MM2, MM3 force fields for fast preoptimization of almost any system.
Quantum Semiempirical:
- Methods: MINDO/3, MNDO, MNDO/d, AM1, PM3, PM5, PM6, RM1, PDDG/MNDO, PDDG/PM3.
- For spectroscopy: ZINDO, INDO/S, CNDO/S, CNDO/S2, CNDO/S3, CNDO/1, CNDO/2, INDO/1, INDO/2.
- Solvent effects for general and organic chemistry (COSMO, Onsager model).
- Linear scaling semiempirical methods for protein optimization and docking.
DFT: D-VWN, D-PW92, B88-PW91, PW91-PW91, B88-P86, B88-LYP.
Orbital Basis: 3-21G, 3-21G(p), 6-31G, 6-31G(p), 6-31G(p,d), DZVP, TZVP.
Molecular Dynamics – over 100 force fields for materials, organic systems, polymers and others:
- Organic: AMBER, CC, Dreiding, KKY, Klein-McDonald, Organic, MM2, MOMEC, OPLS, SPC, TIP.
- Inorganic:
  - 2-Body: Born-Mayer-Huggins, Erkoc, Johnson, Kawamura, Lennard-Jones, Morse.
  - 3-Body: Justo, Marks, Stillinger-Weber, Tersoff.
  - EAM: Ackland, Finnis-Sinclair, Grujicic-Zhou, long range Finnis-Sinclair, Oh-Johnson, Rosato-Guillop-Legrand, tight binding, Voter-Chen, Yang-Johnson.
  - Others: CFF, UFF.

Introduction to SCIGRESS
Get started with practical computational chemistry in a couple of minutes using SCIGRESS.
Conformations of Actinomycin D
The issue of conformational searches is important in drug design and other areas of chemistry. The problem is not trivial for larger, flexible molecules with many degrees of freedom. This video shows how to use SCIGRESS to obtain low energy conformers.
Modeling SN2 Reaction
Modeling of a chemical reaction when the mechanism is known (or assumed) allows verification of that mechanism and study of transition state geometry and other properties. Such calculation can easily be set up and ran using SCIGRESS.
Molecular dynamics Simulations of Graphene
From crystallographic data to Molecular Dynamics trajectory.
Searching for SARS-Cov-2 spike protein inhibitor
Short demo of molecular docking in SCIGRESS software.
pH in Molecular Modeling
A case study on Phenolphthalein UV/VIS spectra using semiempirical quantum calculations in SCIGRESS.

	SCIGRESS Modeling	SCIGRESS Dynamics	SCIGRESS Worksystem
Computational Methods
Molecular Mechanics: MM2, MM3	Yes	Yes	Yes
Semiempirical methods (AM1, PM3, PM6, RM1, PDDG, INDO/S, CINDO/S and more)	Yes	No	Yes
DFT (D-VWN, D-PW92, B88-PW91, PW91-PW91, B88-P86, B88-LYP)	Yes	No	Yes
MD force fields (organic, 2-body, 3-body, EAM and more)	No	Yes	Yes
Types of Calculations
Single point and energy calculations	Yes	No	Yes
Thermodynamic quantities: enthalpies, entropies ...	Yes	No	Yes
Geometry optimization	Yes	Yes	Yes
Conformational analysis	Yes	No	Yes
Spectroscopy - IR, UV-Vis, NMR	Yes	No	Yes
Transition state and reaction searching	Yes	No	Yes
Advanced molecular dynamics	No	Yes	Yes
MD trajectory analysis	No	Yes	Yes
Proteins optimization	Yes	No	Yes
Simple docking	Yes	No	Yes
Multiple and quantum docking	Yes	No	Yes
QSAR	Yes	No	Yes
PubChem Search	Yes	No	Yes
Multiple and batch calculations	Yes	Yes	Yes
GUI to External Engines
Amsterdam Modeling Suite (ADF)	Yes	Yes	Yes
Amsterdam Modeling Suite (BAND)	No	Yes	Yes
AutoDock (Tools and Vina)	Yes	No	Yes
CONFLEX	Yes	No	Yes
GAMESS	Yes	No	Yes
Gaussian	Yes	No	Yes
LAMMPS	No	Yes	Yes
MOPAC	Yes	No	Yes
Quantum ESPRESSO	No	Yes	Yes