SherbyNet - /page/wikibook/entry.mu

Micron Document

<!DOCTYPE html>

<title>MacroModel</title>

</head>

<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">MacroModel</span></span>

</h1>

</header>

/* start https://en.wikipedia.org/ */

.mw-parser-output .infobox-subbox{padding:0;border:none;margin:-3px;width:auto;min-width:100%;font-size:100%;clear:none;float:none;background-color:transparent}.mw-parser-output .infobox-3cols-child{margin:auto}.mw-parser-output .infobox .navbar{font-size:100%}@media screen{html.skin-theme-clientpref-night .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media(min-width:640px){body.skin--responsive .mw-parser-output .infobox-table{display:table!important}body.skin--responsive .mw-parser-output .infobox-table>caption{display:table-caption!important}body.skin--responsive .mw-parser-output .infobox-table>tbody{display:table-row-group}body.skin--responsive .mw-parser-output .infobox-table th,body.skin--responsive .mw-parser-output .infobox-table td{padding-left:inherit;padding-right:inherit}}

/* end https://en.wikipedia.org/ */

</style><table class="infobox vevent"><tbody><tr><th colspan="2" class="infobox-above summary">MacroModel</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Developer(s)</a></th><td class="infobox-data"><a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Schrödinger, LLC</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Initial release</th><td class="infobox-data">1990<span style="display:none"> (<span class="bday dtstart published updated">1990</span>)</span></td></tr><tr style="display: none;"><td colspan="2" class="infobox-full-data"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle" title="Software release life cycle">Stable release</a></th><td class="infobox-data"><div style="margin:0px;">2021-3

</div></td></tr><tr style="display:none"><td colspan="2">

</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Operating_system" title="Operating system">Operating system</a></th><td class="infobox-data"><a href="Linux" title="Linux">Linux</a>, <a href="Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="MacOS" title="MacOS">macOS</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Computing_platform" title="Computing platform">Platform</a></th><td class="infobox-data"><a href="X64" class="mw-redirect" title="X64">x64</a>, <a href="GPGPU" class="mw-redirect" title="GPGPU">GPGPU</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Available in</th><td class="infobox-data">English</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data"><a href="Computational_chemistry" title="Computational chemistry">Computational chemistry</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="Proprietary_software" title="Proprietary software">Proprietary</a>, <a href="Commercial_software" title="Commercial software">Commercial software</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="https://www.schrodinger.com/products/macromodel">www<wbr>.schrodinger<wbr>.com<wbr>/products<wbr>/macromodel</a></span></td></tr></tbody></table>

<p><b>MacroModel</b> is a computer program for <a href="Molecular_modelling" title="Molecular modelling">molecular modelling</a> of <a href="Organic_compound" title="Organic compound">organic compounds</a> and <a href="Biopolymer" title="Biopolymer">biopolymers</a>. It features various <a href="Force_field_(chemistry)" title="Force field (chemistry)">chemistry force fields</a>, plus energy minimizing algorithms, to predict <a href="Molecular_geometry" title="Molecular geometry">geometry</a> and relative <a href="Conformational_isomerism" class="mw-redirect" title="Conformational isomerism">conformational</a> energies of <a href="Molecule" title="Molecule">molecules</a>.<sup id="cite_ref-Mohamadi_1990_1-0" class="reference"><a href="#cite_note-Mohamadi_1990-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> MacroModel is maintained by <a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Schrödinger, LLC</a>.

</p><p>It performs simulations in the framework of <a href="Classical_mechanics" title="Classical mechanics">classical mechanics</a>, also termed <i><a href="Molecular_mechanics" title="Molecular mechanics">molecular mechanics</a></i>, and can perform <a href="Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> simulations to model systems at finite temperatures using <a href="Stochastic_dynamics" class="mw-redirect" title="Stochastic dynamics">stochastic dynamics</a> and mixed <a href="Monte_Carlo_method" title="Monte Carlo method">Monte Carlo</a> algorithms. <i>MacroModel</i> supports <a href="Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="Linux" title="Linux">Linux</a>, <a href="MacOS" title="MacOS">macOS</a>, <a href="Silicon_Graphics" title="Silicon Graphics">Silicon Graphics</a> (SGI) <a href="IRIX" title="IRIX">IRIX</a>, and <a href="IBM_AIX" title="IBM AIX">IBM AIX</a>.

</p><p>The Macromodel software package was first been described in the scientific literature in 1990,<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> and has been subsequently acquired by Schrödinger, Inc. in 2000.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup>

</p>

<div class="mw-heading mw-heading2"><h2 id="Key_features">Key features</h2></div>

/* start https://en.wikipedia.org/ */

.mw-parser-output .div-col{margin-top:0.3em;column-width:30em}.mw-parser-output .div-col-small{font-size:90%}.mw-parser-output .div-col-rules{column-rule:1px solid #aaa}.mw-parser-output .div-col dl,.mw-parser-output .div-col ol,.mw-parser-output .div-col ul{margin-top:0}.mw-parser-output .div-col li,.mw-parser-output .div-col dd{page-break-inside:avoid;break-inside:avoid-column}

/* end https://en.wikipedia.org/ */

</style><div class="div-col" style="column-width: 30em;">

<ul><li><a href="Implicit_solvation" title="Implicit solvation">Implicit solvation</a> (continuum solvation) model, Generalized Born model augmented with the hydrophobic solvent accessible surface area (SA) term (GBSA)<sup id="cite_ref-Still_1990_4-0" class="reference"><a href="#cite_note-Still_1990-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-pmid18422307_5-0" class="reference"><a href="#cite_note-pmid18422307-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup></li>

<li><a href="Force_field_(chemistry)" title="Force field (chemistry)">Force fields</a>: MM2, MM3, <a href="AMBER" title="AMBER">AMBER</a>, <a href="Merck_Molecular_Force_Field" class="mw-redirect" title="Merck Molecular Force Field">Merck Molecular Force Field</a> (MMFF), <a href="OPLS" title="OPLS">OPLS</a></li>

<li><a href="Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></li>

<li><a href="Free_energy_perturbation" class="mw-redirect" title="Free energy perturbation">Free energy perturbation</a></li></ul></div>

<div class="mw-heading mw-heading2"><h2 id="Known_version_history">Known version history</h2></div>

<ul><li>2013: version 10.0</li>

<li>2012: version 9.9.2</li>

<li>2011: version 9.9.1</li>

<li>2010: version 9.8</li>

<li>2009: version 9.7</li>

<li>2008: version 9.6</li>

<li>2007: version 9.5</li>

<li>2006: version 9.1</li>

<li>2005: version 9.0</li>

<li>2004: version 8.5</li>

<li>2003: version 8.1</li></ul>

<ul><li><a href="Comparison_of_nucleic_acid_simulation_software" title="Comparison of nucleic acid simulation software">Comparison of nucleic acid simulation software</a></li>

<li><a href="Comparison_of_force_field_implementations" class="mw-redirect" title="Comparison of force field implementations">Comparison of force field implementations</a></li>

<li><a href="List_of_software_for_molecular_mechanics_modeling" class="mw-redirect" title="List of software for molecular mechanics modeling">List of software for molecular mechanics modeling</a></li>

<li><a href="List_of_software_for_Monte_Carlo_molecular_modeling" title="List of software for Monte Carlo molecular modeling">List of software for Monte Carlo molecular modeling</a></li>

<li><a href="List_of_protein_structure_prediction_software" title="List of protein structure prediction software">List of protein structure prediction software</a></li>

<li><a href="Molecular_design_software" title="Molecular design software">Molecular design software</a></li>

<li><a href="Molecular_modelling" title="Molecular modelling">Molecular modelling</a></li>

<li><a href="Molecule_editor" title="Molecule editor">Molecule editor</a></li>

<li><a href="Abalone_(molecular_mechanics)" title="Abalone (molecular mechanics)">Abalone (molecular mechanics)</a></li>

<li><a href="Ascalaph_Designer" title="Ascalaph Designer">Ascalaph Designer</a></li>

<li><a href="CHARMM" title="CHARMM">CHARMM</a></li>

<li><a href="GROMACS" title="GROMACS">GROMACS</a></li>

<li><a href="MDynaMix" title="MDynaMix">MDynaMix</a></li>

<li><a href="Tinker_(software)" title="Tinker (software)">Tinker (software)</a></li></ul></div>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

/* start https://en.wikipedia.org/ */

.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}

/* end https://en.wikipedia.org/ */

</style><div class="reflist">

/* start https://en.wikipedia.org/ */

.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("./mw/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("./mw/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("./mw/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("./mw/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}

/* end https://en.wikipedia.org/ */

</style><cite id="CITEREFMohamadiRichardGuidaLiskamp1990" class="citation journal cs1">Mohamadi F, Richard NG, Guida WC, Liskamp R, Lipton M, Caufield C, Chang G, Hendrickson T, Still WC (May 1990). "MacroModel - an Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics". <i>J. Comput. Chem</i>. <b>11</b> (4): <span class="nowrap">440–</span>467. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.540110405">10.1002/jcc.540110405</a>.</cite></span>

</li>

<li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><cite id="CITEREFMohamadiRichardsGuidaLiskamp1990" class="citation journal cs1">Mohamadi, Fariborz; Richards, Nigel G. J.; Guida, Wayne C.; Liskamp, Rob; Lipton, Mark; Caufield, Craig; Chang, George; Hendrickson, Thomas; Still, W. Clark (1990-05-01). "Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics". <i>Journal of Computational Chemistry</i>. <b>11</b> (4): <span class="nowrap">440–</span>467. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.540110405">10.1002/jcc.540110405</a>. <a href="ISSN_(identifier)" class="mw-redirect" title="ISSN (identifier)">ISSN</a> <a rel="nofollow" class="external text" href="https://search.worldcat.org/issn/1096-987X">1096-987X</a>.</cite></span>

</li>

<li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.schrodinger.com/about">"Overview | Schrödinger"</a>. <i>www.schrodinger.com</i><span class="reference-accessdate">. Retrieved <span class="nowrap">2017-11-30</span></span>.</cite></span>

</li>

<li id="cite_note-Still_1990-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-Still_1990_4-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFStillTempczykHawleyHendrickson1990" class="citation journal cs1">Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). "Semianalytical treatment of solvation for molecular mechanics and dynamics". <i>J Am Chem Soc</i>. <b>112</b> (16): <span class="nowrap">6127–</span>6129. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Fja00172a038">10.1021/ja00172a038</a>.</cite></span>

</li>

<li id="cite_note-pmid18422307-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-pmid18422307_5-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFGuimarãesCardozo2008" class="citation journal cs1">Guimarães CR, Cardozo M (May 2008). "MM-GB/SA rescoring of docking poses in structure-based lead optimization". <i>J Chem Inf Model</i>. <b>48</b> (5): <span class="nowrap">958–</span>70. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Fci800004w">10.1021/ci800004w</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/18422307">18422307</a>.</cite></span>

</li>

</ol></div></div>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><span class="official-website"><span class="url"><a rel="nofollow" class="external text" href="http://www.schrodinger.com/macromodel">Official website</a></span></span></li></ul></div><div><div class="zim-footer">

This article is issued from <a class="external text" title="Last edited on 2023-06-23" href="https://en.wikipedia.org/wiki/?title=MacroModel&oldid=1161595279">Wikipedia</a>. The text is available under <a class="external text" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en">Creative Commons Attribution-Share Alike 4.0</a> unless otherwise noted. Additional terms may apply for the media files.

</div>

</div></div>

</div>

</main>

</div>

</body></html>