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Chemistry & Life Science

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SCIGRESS

SCIGRESS is a mulitiplatform 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.
Features
  • 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:
Functionality
  • General Chemistry:
    • Building and optimization of geometries of small molecules.
    • Various approaches to conformational analysis.
    • Electronic property calculations (Charges, orbitals, electron density, reactivity towards specific agents and more).
    • Reaction modeling (Transition state search, reaction path calculations).
    • Spectroscopy (UV, IR, NMR).

 
  • Biochemistry & Drug Design:
    • Import, repair and optimize protein structures.
    • Screen libraries of compounds by docking, including quantum docking.
    • Build and apply ADMET Models with QSAR.
  • Materials Science.
Theory Levels
  • Molecular Mechanics:
    • MM2, MM3 force fields for fast preoptimization of almost any system.
  • Quantum Semiempirical:
    • AM1, PM3-6, including solvent effects for general and organic chemistry.
    • ZINDO for spectroscopy.
    • Linear scaling semiempirical methods for protein optimization and docking.
  • DFT:
    • LDA: D-VWN, D-PW92.
    • GGA: B88-LYP, B88-PW91, PW91-PW91, B88-P86.
    • Orbital Basis: DZVP, TZVP, 3-21G, 3-21G(p), 6-31G, 6-31G(p), 6-31G(p,d).
  • 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.
    • Full list of all potentials is available here.
Lineup
 
  SCIGRESS Modeling SCIGRESS Dynamics SCIGRESS Worksystem
Computational Methods
Molecular Mechanics: MM2, MM3 Yes Yes Yes
Semiempirical methods (MINDO, MNDO, AM1, PM3-6, RM1, PDDG, INDO/S, CINDO/S ...) Yes No Yes
DFT (LDA, GGA; DZVP, TZVP, 3-21G - 6-31G(p,d) ...) Yes No Yes
MD force fields (organic, 2-body, 3-body, EAM...) 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 Yes Yes Yes
External engines:
ADFCONFLEXGAMESSGaussianLAMMPSMOPAC and AutoDock (Tools and Vina).
External engines are not distributed with SCIGRESS.


Desktop
  • Windows - 7, 8 and 10 - 32&64 bit.
  • Linux - Ubuntu, OpenSUSE, Debian, Centos - 32&64 bit.
  • MacOS - OS X 10.9 and higher.
  • OpenGL accelerated graphics hardware.

Server
  • Java Runtime Environment is required, either version 7 or 8 would work.
  • SSH server is needed to access SCIGRESS server and for file transfer.
  • For 64-bits version of Linux, 32-bits compatibility libraries need to be installed. In particular, 32-bits glibc and libstdc++.so.6 are needed.

Parallel engines in SCIGRESS
 
  SCIGRESS Windows SCIGRESS Linux SCIGRESS Mac SCIGRESS Server
Semiempirical methods (MO-G) No Yes No Yes
DFT (DGauss) Yes Yes* Yes* Yes*
Proteins optimization (LocalSCF) Yes Yes Yes Yes
Advanced molecular dynamics (MD-ME) No Yes No Yes
* - Some computational algorithms are parallelized.

 

SCIGRESS

SCIGRESS is a mulitiplatform 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:
  • General Chemistry:
    • Building and optimization of geometries of small molecules.
    • Various approaches to conformational analysis.
    • Electronic property calculations (Charges, orbitals, electron density, reactivity towards specific agents and more).
    • Reaction modeling (Transition state search, reaction path calculations).
    • Spectroscopy (UV, IR, NMR).

 
  • Biochemistry & Drug Design:
    • Import, repair and optimize protein structures.
    • Screen libraries of compounds by docking, including quantum docking.
    • Build and apply ADMET Models with QSAR.
  • Materials Science.
  • Molecular Mechanics:
    • MM2, MM3 force fields for fast preoptimization of almost any system.
  • Quantum Semiempirical:
    • AM1, PM3-6, including solvent effects for general and organic chemistry.
    • ZINDO for spectroscopy.
    • Linear scaling semiempirical methods for protein optimization and docking.
  • DFT:
    • LDA: D-VWN, D-PW92.
    • GGA: B88-LYP, B88-PW91, PW91-PW91, B88-P86.
    • Orbital Basis: DZVP, TZVP, 3-21G, 3-21G(p), 6-31G, 6-31G(p), 6-31G(p,d).
  • 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.
    • Full list of all potentials is available here.
 
  SCIGRESS Modeling SCIGRESS Dynamics SCIGRESS Worksystem
Computational Methods
Molecular Mechanics: MM2, MM3 Yes Yes Yes
Semiempirical methods (MINDO, MNDO, AM1, PM3-6, RM1, PDDG, INDO/S, CINDO/S ...) Yes No Yes
DFT (LDA, GGA; DZVP, TZVP, 3-21G - 6-31G(p,d) ...) Yes No Yes
MD force fields (organic, 2-body, 3-body, EAM...) 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 Yes Yes Yes
External engines:
ADFCONFLEXGAMESSGaussianLAMMPSMOPAC and AutoDock (Tools and Vina).
External engines are not distributed with SCIGRESS.


Desktop
  • Windows - 7, 8 and 10 - 32&64 bit.
  • Linux - Ubuntu, OpenSUSE, Debian, Centos - 32&64 bit.
  • MacOS - OS X 10.9 and higher.
  • OpenGL accelerated graphics hardware.

Server
  • Java Runtime Environment is required, either version 7 or 8 would work.
  • SSH server is needed to access SCIGRESS server and for file transfer.
  • For 64-bits version of Linux, 32-bits compatibility libraries need to be installed. In particular, 32-bits glibc and libstdc++.so.6 are needed.

Parallel engines in SCIGRESS
 
  SCIGRESS Windows SCIGRESS Linux SCIGRESS Mac SCIGRESS Server
Semiempirical methods (MO-G) No Yes No Yes
DFT (DGauss) Yes Yes* Yes* Yes*
Proteins optimization (LocalSCF) Yes Yes Yes Yes
Advanced molecular dynamics (MD-ME) No Yes No Yes
* - Some computational algorithms are parallelized.