ZMM SOFT

ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies.

Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed.

• ZMM runs on Windows 2000, XP, 7, 10, Mac-OS, UNIX, and Linux
• ZMM can be used via the command-line interface
• ZMM can also be used at Windows via a graphical user interface

Scientific Board

Ten reasons to try ZMM

1. ZMM is universal: you can model drugs, peptides, proteins, nucleic acid, and ligand-receptor complexes
2. ZMM is fast. It minimizes energy in the space of generalized coordinates (Zhorov, 1981; Zhorov, 1982) and employs highly efficient method of Monte Carlo minimization (Li and Scheraga, 1987)
3. ZMM is flexible: large number of controls can tune ZMM for a specific task
4. ZMM is user-friendly. It includes a graphic interface MVM and can also be used with any molecular graphics program, e.g. RASMOL and PYMOL
5. ZMM is easy to use: you can import molecular structure from a PDB file in one command or mutate a protein in one keystroke
6. ZMM is easy to learn. It includes comprehensive description and hundreds of examples
7. ZMM integrates 30+ years of experience in molecular modeling of biomolecular systems
8. 200+ publications on ZMM-based studies are available
9. ZMM runs under Windows, UNIX, and Linux
10. Parallel ZMM for UNIX and Linux is available

More about ZMM

ZMM implements various methods for conformational search:

• Energy minimization in generalized coordinates (Zhorov, 1981, 1983)
• Nested rotations with building multidimensional grids
• Monte Carlo minimization (Li & Scheraga, 1987)
• Monte Carlo minimization (MCM) in the space of scaled collective variables (Noguti & Go, 1985; Maurer et al., 1999)
• Biased MCM (Abagyan & Totrov, 1994)
• Nested MCM protocol (unpublished)
• Stochastically restrainable MCM (unpublished)
• Computing MC-minimized energy profile of a ligand in a protein (Zhorov and Lin, 2000)
• Computing multidimensional MC-minimized energy map of a ligand in a protein (unpublished)

ZMM includes well-known force fields:

• AMBER
• ECEPP/2
• MM2
• V.G. Dashevskii (1970)
• Zhurkin et al. (1983)

Publications

ZMM was used as the major modeling tool in 300+ studies, including

• Possible Mechanism of Ion Selectivity in Eukaryotic Voltage-Gated Sodium Channels (Zhorov, 2021)
• Intersegment Contacts of Potentially Damaging Variants of Cardiac Sodium Channel (Korkosh et al, 2021)
• Atomic Mechanisms of Timothy Syndrome-Associated Mutations in Calcium Channel Cav1.2 (Korkosh et al.m 2019)
• Phenylalkylamines in calcium channels: computational analysis of experimental structures (Tikhonov et al, 2020)
• Potentiation and Block of ASIC1a by Memantine (Shteinikov et al., 2018)
• Sodium channels with drugs and toxins (Tikhonov and Zhorov, 2017; Korkosh et al., 2014)
• Chloride channels with ligands (Maleeva et al., 2017; Zhorov & Bregestovski, 2000)
• Docking insecticides in sodium channels Wu et al., 2017; Du et al., 2013)
• Protein modeling with MTSET-substituted cysteines (Bruhova & Zhorov, 2010)
• Flexible ligand docking (Garden & Zhorov, 2010)
• Docking Ca2+ ions in flexible proteins (Cheng et al., 2010)
• L-type Ca2+ channel with phenylalkylamines (Cheng et al. 2009)
• L-type Ca2+ channel with dihydropyridines (Tikhonov and Zhorov, 2009)
• Na+ channel with insecticides (Du et al., 2009)
• Polyamine toxins in ionotropic glutamate receptors (Nelson et al., 2009)
• Na+ channel with batrachotoxin (Wang et al., 2007)
• Local anesthetics: access and binding in Na+ channel (Bruhova et al., 2008)
• L-type Ca2+ channel with benzothiazepines (Tikhonov and Zhorov, 2008)
• Slow Inactivation and ligand binding in Na+ channel (Tikhonov and Zhorov, 2007)
• Correolide in Kv1.3 channel ( Bruhova and Zhorov, 2007)
• d-Tubocurarine in K+ channel ( Rossokhin et al., 2006)
• Mechanism of Na channel agonists (Tikhonov and Zhorov, 2005; Wang et al., 2006)
• Local anesthetics and benzocaine in Na+ channel (Tikhonov al., 2006)
• Predicting the pore geometry of the Shaker channel and mechanism of its block by Cd2+ ( Bruhova and Zhorov, 2005)
• Predicted geometrical features of the channel agree with the later x-ray structure (Long et al., 2005)
• Mapping steroids binding site in an enzyme ( Blanchet et al., 2005)
• Modeling selectivity filter of sodium channel (Tikhonov and Zhorov, 2005)
• Large-scale conformational transitions in a protein (Tikhonov and Zhorov, 2004)
• Noncompetitive antagonism in a nicotinic acetylcholine receptor (Tikhonov et al., 2004)
  • This paper shows, in particular, that a protein model made with ZMM and published in 1998 predicted important features of the experimental structure published in 2003)
• Simulation of antifreeze proteins at ice (Jorov et al. 2004)
• Ligand action in voltage-gated ion channels (Zhorov and Tikhonov, 2004)
• Block of NMDA channels ( Bolshakov et al., 2003)
• Agonist action in Ca2+ channels (Yamaguchi et al., 2003)
• Block of glutamate receptors (Tikhonov et al., 2002)
• L-type calcium channel with ligands (Zhorov et al., 2001)
• Structure and function of testosterone-binding enzyme (Nahoum et al., 2001)
• G-protein coupled receptors with ligands (Zhorov & Ananthanarayanan, 2000)
• Structure-activity relationships of polyamine amide toxins (Tikhonov et al., 2000)
• Systematic search for the steroid-binding site in an enzyme (Zhorov and Lin., 2000)
• Modeling of ion channels of glutamate receptors ( Tikhonov et al., 1999)
• Modeling of collagen (Milchevski et al., 1999)
• Nicotinic acetylcholine receptor channel with blockers ( Tikhonov & Zhorov, 1998 )
• Modeling of a synthetic calcium channel with ligands (Zhorov & Ananthanarayanan, 1996)
• Pheromones (Tsendina et al., 1989; Bykhovskaya and Zhorov, 1996)
• Conformation-activity relationships of adrenergic drugs (Zhorov et al., 1975-1985)

Downloads

Click the followings to download ZMM:

• ZMM-2022a for Windows
• ZMM-2022b for Windows
• • Installing ZMM on Windows (you need to download both a & b files)

    Installing ZMM on Windows

    1. Download file zmm-mvm_Year_Month_Date_a_setup.exe
    2. Download file zmm-mvm_Year_Month_Date_b_setup.exe
    3. Temporary disable antivirus software on windows
    4. Click zmm-mvm_Year_Month_Date_a_setup.exe and follow instructions
    5. Click zmm-mvm_Year_Month_Date_b_setup.exe and follow instructions
    6. Default installation location is c:/zmm/
    7. To test ZMM, go to zmm/Test/ and click "0_run". Upon completion of the test edit/inspect the various .dif files in the Test/ directory. The listed .dif files should be within the size of 1000 bytes. You should see neither *fail files, nor ZMM_error files. Files *.dif shows the output difference between your computer and ZMM-developers computer. The difference may occur due to specific hardware configurations. In case of big difference(s), please contact zmmsoft.ca.
    8. Once satisfied with installation, click "0_clean" to cleanup all files generated during testing.
    9. Instructions are contained in ZMM_HOME/exe/zmm_help.chm
    10. Instructions for viewer (MVM) are contained in ZMM_HOME/MVM/mvm_HELP.chm

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• ZMM-2022 for GNU/Linux (x86_64)
• • Installing ZMM on Linux

    Installing ZMM on Linux

    1. Create a home directory for ZMM. It may have any name and any location. The following commands assume that the ZMM home directory is ~/zmm/
    2. Put file zmm.tar.gz in ~/
    3. Go to directory ~/
    4. Type: gunzip zmm.tar.gz
    5. Type: tar xpf zmm.tar
    6. Specify path to folder ~/zmm/exe/ (See Examples below).
    7. Set environmental variable ZMM_HOME (See Examples below)
    8. To test ZMM, go to zmm/test/ and type "run". or use your queue submision tool to submit run. Upon completion of the test, type "analyse". You should see neither *fail files, nor ZMM_error files. Files *.dif will show the output difference between your computer and ZMM-developers computer. The difference may occur due to specific hardware configurations. In case of big difference(s), please contact ZMMSoft.
    9. Use PC/Windows to read and search zmm_help.chm help file.

    Examples:

    tcsh: add the following two lines to file .cshrc

    setenv ZMM_HOME ~/zmm/ set path=(~/zmm/exe $path)

    bash: add the following two lines to file .bashrc

    export ZMM_HOME=${HOME}/zmm/ export PATH=${PATH}:${HOME}/zmm/exe

    The above lines may vary depending on the operating system and command interpreter. Contact your system administrator for details.

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• ZMM-2022_a for Mac (x86_64)
• ZMM-2022_b for Mac (x86_64)
• • Installing ZMM on MacOS (you need to download both files)

    Installing ZMM on MacOS

    1. Put file zmm.tar.gz in your home directory. i.e. /Users/xxxx, where xxxx is your user name on the system.
    2. Type: gunzip zmm.tar.gz
    3. Type: tar xpf zmm.tar
    4. The default home directory for ZMM is ~/zmm/. Where ~ is your $HOME. If you want to install ZMM in other location, put zmm.tar.gz in that directory and execute steps 1 to 3.
    5. Specify path to folder ~/zmm/exe/ (See Notes below)
    6. Set environmental variable ZMM_HOME (See Notes below)
    7. To test ZMM, go to zmm/Test/ and type "run". Upon completion of the test, type "analyse". You should see neither *fail files, nor ZMM_error files. Files *.dif will show the output difference between your computer and ZMM-developers computer. The difference may occur due to specific hardware configurations. In case of big difference(s), please contact zmmsoft.ca.

    Notes:

    bash: add the following two lines to file .bashrc

    export ZMM_HOME=${HOME}/zmm/ export PATH=${PATH}:${HOME}/zmm/exe

    The above lines may vary depending on the operating system and command interpreter. Contact your system administrator for details.

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