HyperChem软件
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3D分子图形显示工具 (RasMol and OpenRasMol)(免费)AMBER (分子力学力场模拟程序)autodock (分子对接软件)(免费)GROMACS (分子动力学软件)(免费)GULP (General Utility Lattice Program)(免费)NIH分子模拟中心的化学软件资源导航(Research Tools on the Web) X-PLOR (大分子X光晶体衍射、核磁共振NMR的3D结构解析)(免费)高通量筛选软件PowerMV (统计分析、分子显示、相似性搜索等)(免费)化合物活性预测程序PASS(部分免费)计算材料科学MathubC4:Cabrillo学院化学可视化项目以及相关软件(免费)Databases and Tools for 3-D Protein Structure Comparison and Alignment(三维蛋白质结构对比)(免费)Democritus (分子动力学原理演示软件)DPD应用软件cerius2(免费)EMSL Computational Results DataBase (CRDB)MARVIN'S PROGRAM (表面与界面模拟)(免费)XLOGP(计算有机小分子的脂水分配系数)(免费)量子化学软件中文网美国斯克利普斯研究院:金属蛋白质结构和设计项目(免费) /(免费)3D Molecular Designs (蛋白质及其他3D分子物理模型快速成型技术)3D-Dock Suite Incorporating FTDock, RPScore and MultiDock (3D分子对接)(免费)AMSOL (半经验量子化学计算)(免费)Amsterdam Density Functional (ADF, 第一原理电子结构计算) Bilbao晶体学服务器(免费)BOSS (蒙特卡罗模拟软件)CADPAC (剑桥量子化学计算软件)(免费)Car-Parrinello分子动力学(CPMD, ab-initio分子动力学计算软件)(免费)CHARMM (大分子分子力学模拟计算软件)(部分免费)Chem2Pac package (A computational Chemistry Integrator)(免费) ChemTK Lite (QSAR软件)(免费)Chemweb计算化学在线工具:GAMESS(免费)Clebsch-O-Matic (在线计算器)(免费)Collaborative Computational Projects (协同计算计划) COLUMBUS (量化从头计算分子电子结构程序集)(免费) CrystalMaker Software (晶体结构可视化软件)DL_POLY (分子动力学模拟软件)(免费)DockVision (分子对接程序)(部分免费)DPMTA (分子动力学并行模拟软件)(免费)Dr. Pablo Wessig 研究小组开发的计算化学软件(免费)eHiTS: Electronic High Throughput ScreeningEMSL Gaussian Basis Set Order Form(免费)GAMESS-UK (分子电子结构计算软件)GAMESS: The General Atomic and Molecular Electronic Structure System(免费)Genebrowser (生物技术、基因治疗资源导航)Glide (分子对接程序)GROMOS (通用分子动力学软件包)(部分免费)HyperChem (分子模拟)Interprobe Chemical Services (分子模型化软件)Jmol (分子可视化软件)(免费)List of Computationally Sick Species (ab initio计算出现问题的物质、方法)MacroModel (分子力学计算程序)MARDIGRAS和CORMA (弛豫矩阵分析)(免费)MCPRO (用于蛋白质和核酸的蒙特卡罗模拟软件)MDRANGE (分子动力学计算ion ranges)(免费)MDynaMix (分子动力学计算软件)(免费)MidasPlus (分子建模软件, 美国加利福尼亚大学旧金山分校计算机图形实验室开发)MOE(分子模拟应用环境、方法开发平台)MOLMOL (生物大分子3D结构分析和显示、NMR结构解析)(免费) MolPOV 2.0.8 (一个将PDB文件转为POV-Ray文件的软件)(免费) MOLPRO 量子化学软件包 (用量化从头方法计算分子电子结构)(免费) Mopac 2002 (通用半经验量子力学程序)NAMD (并行分子动力学计算软件)(免费)Norgwyn Montgomery (化学软件公司)NWChem (计算化学软件包)OpenEye (快速计算分子的静电性质、形状)ORAC (用于模拟溶剂化生物分子的分子动力学计算程序, 意大利佛罗伦萨大学)(免费)ORTEP-III (美国橡树岭国家实验室晶体结构可视化--热椭圆体绘图程序)(免费)OSIRIS Property Explorer (LogP, 溶解度、成药可能性预测)(免费) PAPA (计算粒状物料的三维并行分子动力学计算程序)(免费) PETRA (反应性参数预测,包括生成焓、键离解能等)(部分免费) PharmTree (3D药效团生成和化合物分类)Pipeline Pilot (药物发现集成平台)PMDS (并行分子动力学模板库)(免费)PreADMET (ADMET预测)Protein Domain Motion Analysis Software: DynDom (蛋白质分析软件)(免费)ProtoMol (分子动力学并行计算软件)(免费)PSI3量子化学软件包(量化从头计算)(免费)Q-Chem (量子化学计算软件包)SGI应用于化学、生物信息学的软件、硬件产品SIGMA (分子动力学相关软件)SimBioSys (药物设计软件SPROUT)SMILECAS 数据库 (描述分子结构、子结构和复合结构的线性编码系统)SURFNET (量子化学计算程序)(免费)Sweet (依据标准命名方法和分子顺序建立糖类三维模型)Swiss PDB Viewer (PDB蛋白质结构可视化软件)SYBYL/Base(分子模拟和药物发现平台)TINKER (分子设计软件)(免费)UCSF Chimera (可扩展的, 交互式分子图形程序)(免费)VAMP/VASP (采用从头计算量子力学的分子力学)(免费)VHMPT (螺旋膜蛋白拓扑结构显示与编辑程序)(免费)Virtual Molecular Dynamics Laboratory (分子动力学软件)(免费) voidoo(空腔探测软件)(免费)WAM: Web Antibody Modeling (抗体模型构建)(部分免费) WebMO (基于3W界面的计算化学软件包)(免费)并行分子动力学模拟软件DoD-TBMD(免费)大分子对接程序Hex(免费)大规模原子(分子)并行模拟器 LAMMPS(免费)单晶和粉末衍射合作计算项目开发的免费软件(CCP14)(免费)蛋白质分子动力学模拟软件:CONCOORD(免费)蛋白质模拟资源导航,美国橡树岭国家实验室ORNL分子的物理化学性质在线计算 (用在基于结构的药物设计, 可计算logP, PSA,等)(免费)化合物3D结构VRML文件的自动生成(免费)化学中的常用计算机软件与资源(免费)化学资源工具箱(免费)计算机模拟的分子运动图像集(DSMM)(免费)可下载的教学软件(伦敦大学玛丽女王学院化学系提供)(免费)量子化学网美国华盛顿州立大学化学系:无机化学教学资源美国加州大学圣地亚哥分校所开发的化学软件 (化学反应计算、分子建模和可视化)美国康奈尔大学理论中心计算生物服务单元提供的免费软件 (计算生物与化学方面)(免费)美国马里兰大学:生物技术研究所Gilson研究小组美国能源部Ames实验室:经典分子动力学软件AL_CMD(免费)免费远程计算:贵州大学GHPCC量子化学从头计算系统(免费)模拟蛋白质的并行分子动力学计算程序EGO(免费)牛津大学:抗癌药物分布式计算项目 Screensaver Lifesaver欧洲科学基金资助项目:分子模拟所面临的挑战 (Simu: Challenges in Molecular Simulations)生物大分子结构分析和确认系列软件(美国加州大学圣地亚哥分校大分子结构计算研究中心开发)(免费)牙买加西印度大学Mona分校化学系所开发的免费软件(免费)应用于双原子分子的数值Hartree-Fock程序(免费)原子轨道3维模拟演示。
计算机与化学教学摘要:本文介绍了计算机在化学教学中的一些应用,包括互联网上可用的化学资源,教学中的常用软件,以及计算机辅助教学等,对化学教师和化学专业的学生都有一定的帮助。
关键词:化学教学计算机软件随着科学技术的飞速发展,计算机技术、网络技术及信息技术在化学学科中的不断渗透、不断融合,计算机在现代化学教学中扮演着越来越重要的角色,给化学教学带来了极大的便利。
1. internet上的化学资源互联网上常见的化学资源类型有:化学教学课件和教学素材,化学教学优秀教案,化学教学参考资料,网络电子图书、电子杂志和期刊,网络教程等。
以前的文献[1-3]对此有较详细的描述,这里不再赘述。
2.化学教学中的常用软件计算机软件可以在人们的工作、学习与研究中协助我们更快、更好、更方便地工作,化学工作者经常用到的软件通常可分为一般软件和化学专业软件。
2.1一般软件2.1.1 powerpoint[4]powerpoint是microsoft公司开发的用于制作和演示幻灯片的软件,能够制作出集文字、图形、图像、声音、动画及视频剪辑等多媒体元素于一体的演示文稿,以形象生动、图文并茂的形式将你要表达的内容在计算机或大屏幕上动态地表现出来。
2.1.2 authorware[4]authorware是macromedia公司开发的一种多媒体软件制作工具。
它与传统的计算机程序设计语言不同,只要通过对图标的调用来编辑一些控制程序走向的流程图,将文字、图像、图形、动画、声音、视频等各种多媒体项目数据汇集在一起,赋予其人机交互功能,从而达到多媒体软件制作的目的。
2.1.2 excel[5]microsoft excel软件是微软公司开发的功能强大的电子表格管理软件,由于其丰富的库函数和强大的逻辑判断、计算功能,使用microsoft excel软件处理实验数据,具有方便、快捷、准确度高等优点。
我们运用这个软件解决化学理论教学中的曲线绘制、数据处理、实验标准曲线制作等问题。
dmol中设置磁构型有如下几种方法:1)可以更改自旋多重度,根据体系的未配对电子数来更改多重度,S=n+1,比如说体系的未配对电子数是2个,那么自旋多重度只能取1,3,5,7......,算完后,比较能量2)在modify里更改高低自旋的搭配来实现不同磁构型,不过只能是共线型的,dmol不能考虑非共线磁结构。
Enck: make p1后设置指定的反铁磁排布,然后再寻找回对称性,但在寻找对称性之前要在options里把formalspin 勾上。
接着把Use formal spin as initial前打√,然后再算Stou: 在优化自旋的时候,初值一定要取的合适,不然得到的自旋结果很可能是不正确的。
原子少的体系可能还不要紧,但是多原子体系的话很容易出现这样的问题Enck: 在bulid-symmetry-find symmetry里,就会看到options。
这时候,Use formal spin as initial前打√是必须的,作用是启用前面的那些预设自旋encke,非常感谢你的帮助,另外额外想问你一个问题,对于自旋的设置,我一直都搞不太明白。
比如对于我研究的氧化铁体系,我在structure中导入结构,make P1 后,在modify/electronic configuration中设置了每一层原子不同的自旋方向,我的问题是:当我打开electronic configuration对话框,里面不是有个formal charge吗?那个值显示的是3,是不是就是氧化铁中的铁的化合价?然后如果点automatic,就自动变成2了,相应的low spin 和high spin也相应的发生变化,2代表什么?究竟应不应该在automatic前打上√呢?对于spin state中改选high还是low我也搞不清楚,我通常都是分别计算这两种情况下的能量看哪个能量低就选哪个,我不知道这样做可行不可行?期待你的答复,万分感激!Enck: 如果不是要求非常非常高,也就是正常情况下,计算软件本身就会对元素的基本性质进行判断,你选择自动加载电荷即可。
河北师范大学计算量子化学研究所蔡新华教授量子化学在线教学.100/qc/lzhx-0.htmHyperChem 程序及其应用一、HyperChem 程序的运行环境HyperChem 程序包,用C++写源程序,具有工作站、微机等不同的版本,作为教学示例,我们向大家介绍适用于微机运行的程序版本。
可以通过网络选购HyperChem程序包,也可以免费下载演示版本以供学习只用,现在该公司提供的最新版本为V6.0。
该公司的网址为:该公司与98年诺贝尔奖金得主Pople的关系可以参看其网页有关介绍。
1、软件环境Windows95、Windows98或Windows2000系统。
2、硬件环境486以上的微机,内存应在8M以上,硬盘至少有32M以上自由空间。
为了能够以最佳方式显示分子图像,最好有VGA以上显示器。
3、程序安装使用该程序应注意程序版权(注册)。
安装程序默认子目录为:C:\hyper6安装完成后,该目录可以看到如下文件,其中,绿色烧杯为执行程序图标。
有关该程序的使用说明、参考手册等全套文档均可免费获得。
二、程序基本使用方法我们以演示版本为例,说明该程序的基本使用方法。
1、启动程序在屏幕上,双击绿色烧杯可以得到如下画面:点击 Try进入工作区窗口窗口各部分功能简介标题名称:最大、最小化、退出按钮菜单条:FILE、EDIT、BUILD、SELECT、DISPLAY、DATABASE、SETUP 、COMPUTE、CANCEL、SCRIPT、HELP工具条:工作区:状态行:2、打开已存在的数据文件File-Open选择分子图形的显示方式Display- Labels可以选择原子、化学键等标记方式:Dispay-RenderingRenderings-BallsRendering—Balls and Cylinders3、建立计算分子的数据文件以丁二烯为例:选择Build-Default Element可以显示指定元素的基本性质:选择绘图工具后,得到碳碳骨架。
dmol中设置磁构型有如下几种方法:1)可以更改自旋多重度,根据体系的未配对电子数来更改多重度,S=n+1,比如说体系的未配对电子数是2个,那么自旋多重度只能取1,3,5,7......,算完后,比较能量2)在modify里更改高低自旋的搭配来实现不同磁构型,不过只能是共线型的,dmol不能考虑非共线磁结构。
Enck: make p1后设置指定的反铁磁排布,然后再寻找回对称性,但在寻找对称性之前要在options里把formalspin 勾上。
接着把Use formal spin as initial前打√,然后再算Stou: 在优化自旋的时候,初值一定要取的合适,不然得到的自旋结果很可能是不正确的。
原子少的体系可能还不要紧,但是多原子体系的话很容易出现这样的问题Enck: 在bulid-symmetry-find symmetry里,就会看到options。
这时候,Use formal spin as initial前打√是必须的,作用是启用前面的那些预设自旋encke,非常感谢你的帮助,另外额外想问你一个问题,对于自旋的设置,我一直都搞不太明白。
比如对于我研究的氧化铁体系,我在structure中导入结构,make P1 后,在modify/electronic configuration中设置了每一层原子不同的自旋方向,我的问题是:当我打开electronic configuration对话框,里面不是有个formal charge吗?那个值显示的是3,是不是就是氧化铁中的铁的化合价?然后如果点automatic,就自动变成2了,相应的low spin 和high spin也相应的发生变化,2代表什么?究竟应不应该在automatic前打上√呢?对于spin state中改选high还是low我也搞不清楚,我通常都是分别计算这两种情况下的能量看哪个能量低就选哪个,我不知道这样做可行不可行?期待你的答复,万分感激!Enck: 如果不是要求非常非常高,也就是正常情况下,计算软件本身就会对元素的基本性质进行判断,你选择自动加载电荷即可。
HyperChem基本操作单点计算单点计算,仅仅执行势能曲面上的一个单个点的计算。
例如对一个双原子分子来说,这可能是在点a原子间距离R=2.0埃的计算。
单点计算的结果给出系统在当前几何构型的势能,以及那个点的梯度。
在点b,c,d,或e的单点计算可能将给出更高的能量。
如果在关键的部分取足够多的点,利用Origin或者Matlab等数学工具软件,就能描出势能曲线,从而精确算出离解能De和核平衡距离re,利用公式就能得到震动参数ωe。
对多原子系统来说,状况更加复杂,但是本质是一样的。
Orbital中显示的轨道信息Alpha & Beta显示选择的轨道是alpha自旋还是beta自旋。
LUMO+显示选择轨道相对于LUMO的位置关系。
例如,选择能量在LUMO之上的轨道,文本框依次显示+1,+2,+3......;如果选择能量低于LUMO的轨道,文本框显示-1,-2,-3......。
HOMO-显示选择轨道相对于HOMO的位置关系。
例如,选择能量在HOMO之上的轨道,文本框依次显示-1,-2,-3......;如果选择能量低于HOMO的轨道,文本框显示+1,+2,+3......。
Number显示从能量最低轨道开始的选择轨道绝对数值。
对于UHF计算,轨道的alpha和beta列编号分开显示,对HOMO-和LUMO+选项也是这样。
Energy以eV为单位显示选择轨道的能量。
Symmetry显示选择轨道的不可约表示。
Labels在轨道显示窗口中,显示每个轨道的电子占据情况和每个轨道的能量。
按照约定俗成,向上的箭头代表alpha自旋,向下的箭头代表beta自旋。
对于RHF计算,最大轨道占据是2;对于UHF计算,最大轨道占据是1。
Zoom Out和轨道的放大如果轨道间距太密,在使用Labels时,文字符号会重合在一起,看起来很不方便。
通过鼠标左键圈出一个或相邻几个选择的轨道,这些轨道就会被放大。
放大之后,Zoom Out选项可以在窗口中重新回到显示全部轨道范围。
献给初学高斯并挣扎的同志们…(经常总结确实能学到很多东西)Gaussian相关的免费软件(Gaussview除外)图形分析界面(本文为免费文档,请勿将此文件强加任何收费限制 )(Second edited by 废man 2010-09-25 12:39 )欢迎大家继续补充,请在上面的括号内加上自己的名字并注明修改日期,并将补充的文字用红色字体标明,谢谢!除了Gaussian使用的软件外,/software提到了众多的分子模拟软件,欢迎大家去看看。
1.Molden http://www.cmbi.ru.nl/molden/(免费)电子密度是由荷兰的G. Schaftenaar于1991年开发的从头算Gamess,Gaussian和半经验Mopac/Ampac 接口的电子密度显示软件,通常运行于Unix环境下,Windows下需要安装X-WinPro来支持其运行。
Molden可以显示分子轨道、电子密度等值线图或3D格点图等,同时可以输出postscript、XWindows、VRML、Povray、OpenGL、tekronix4014、hpgl和hp2392格式的文件,Molden 可以读取chemx、PDB、mopac/ampac以及其它一些格式的文件。
Molden有方便的Z矩阵编辑器,可以方便的对构建的分子进行操作。
对于高斯而言,与Molden结合使用的时候需要使用IOP(6/7=3)关键字。
草氨酸钠静电势的例子参考/~kalju/chem226/public/task2A.html2.Molekel http://molekel.cscs.ch/(免费)分子模型和电子结构显示的免费工具,支持的分子结构计算程序输出文件格式有:GAUSSIAN、GAMESS-US、ADF、ZINDO、MOS、HONDO, Jaguar, MOLPRO, HyperChem, Mopac, NWChem和QChem等和NBO等。
HyperChem软件中Script的常用语句注解1. 计算方法及参数设定calculation-method item计算方法设定item: MolecularMechanics, SemiEmpirical, AbInitio, DFT molecular-mechanics-method item分子力学方法设定item: mm+, amber, bio+, opls, amber94, charmm22, tndo optim-max-cycles x优化最大迭代次数x设定optim-convergence goal 优化收敛目标goal设定optim-converged返回是否收敛(true/false)optim-algorithm item 优化算法设定item: PolakRibiere, NewtonRaphson, etc.assign-basisset item abinitio计算基组设定item: 3-21G, STO-3G, etc.semi-empirical-method item半经验计算方法设定item: am1, pm3, extendedhuckel, cndo, indo, zindos, mndod, tndo, etc.accelerate-scf-convergence true/false 是否加速SCF收敛scf-convergence goal SCF收敛目标goal设定max-iterations n SCF计算的最大迭代次数n设定2. 计算结果输出omsgs-to-file filename 将信息输出到filename文件append-omsgs-to-file filename 将信息追加到filename文件omsgs-not-to-file 关闭输出文件query-response-has-tag yes/no 提取的信息回显开关query-value HSV提取系统数据结构中的信息并单行输出HSV: current-file-name, coordinates,dipole-moment, dipole-moment-componentstotal-energy, heat-of-formation,scf-binding-energy, scf-core-energy, scf-electronic-energy start-logging HyperChem运行记录开启stop-logging HyperChem运行记录关闭export-property-file filename将分子轨道信息写入filename文件3. 分子结构及其文件操作file-format item定义分子结构文件格式item: hin, mol, zmt, ent, skc, xyz, ml2open-file filename 读入filename分子结构文件write-file filename 将分子结构写入filename文件menu-build-add-hydrogens 给分子加氢menu-build-model-build 给分子加氢并规格化do-optimization 进行优化操作do-single-point 进行单点计算do-molecular-dynamics进行分子动力学操作4. 屏幕显示设置screen-refresh-period n屏幕刷新周期atom-labels item原子标识设定item: none, number, symbol, name, charge, etc.show-hydrogens yes/no 分子中氢显示开关show-multiple-bonds yes/no分子中重键显示开关request string弹出窗口并显示由双引号表达的字符串string 5. 其它read-script filename读取名为filename的script文件exit-script 退出script实例: example.scrcalculation-method molecular-mechanicsmolecular-mechanics-method mm+optim-max-cycles 2048optim-convergence 0.1optim-algorithm PolakRibiereomsgs-to-file results.txtquery-response-has-tag nofile-format molopen-file 000A-0001.molmenu-build-model-builddo-optimizationquery-value total-energyfile-format zmtwrite-file 000A-0001.zmtomsgs-not-to-fileexit-script附: HyperChem State Variables (HSV)abinitio-buffer-size: Variable, Read/Write.Type: integer in range (1 .. 2147483647).Two electron integral buffer size.abinitio-calculate-gradient: Variable, Read/Write.Type:boolean.Enable Ab Initio gradient calculation (Single Point only).abinitio-cutoff: Variable, Read/Write.Type: float in range (0 .. 1e+010).Two electron integral cutoff.abinitio-d-orbitals: Variable, Read/Write.boolean.Type:Either five (False) or six (True).abinitio-direct-scf: Variable, Read/Write.boolean.Type:Enable Ab Initio Direct SCF calculation.abinitio-f-orbitals: Variable, Read/Write.boolean.Type:Either seven (False) or ten (True).abinitio-integral-format: Variable, Read/Write.Type: enum(raffenetti, regular).Either regular or raffenetti.abinitio-integral-path: Variable, Read/Write.string.Type:Path for storing integrals.abinitio-mo-initial-guess: Variable, Read/Write.Type: enum(core-hamiltonian, projected-huckel, projected-cndo, projected-indo).Either core-hamiltonian, projected-huckel, projected-cndo, projected-indo. abinitio-mp2-correlation-energy: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 correlation energy.abinitio-mp2-frozen-core: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 frozen core.abinitio-scf-convergence: Variable, Read/Write.Type: float in range (0 .. 100).SCF Convergence for Ab Initio.abinitio-use-ghost-atoms: Variable, Read/Write.boolean.Type:Include or ignore ghost atoms.accelerate-scf-convergence: Variable, Read/Write.Type:boolean.Whether to use DIIS procedure.add-amino-acid: Command.Arg list: string.String-1 gives the name of an amino acid residue to add to the system.add-nucleic-acid: Command.Arg list: string.String-1 names the nucleotide to add to the current system.align-molecule: Command.Arg list: .Align the inertial axes of the molecular system.align-viewer: Command.Arg list: enum(x, y, z, line).Align the viewer's line-of-sight with the indicated axis or LINE.allow-ions: Variable, Read/Write.Type:boolean.Whether to allow excess valence on atoms.alpha-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.alpha-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.amino-alpha-helix: Command.Arg list: (void).Subsequent additions of amino acid residues are to use alpha-helix torsions. amino-beta-sheet: Command.Arg list: (void).Subsequent additions of amino acid residues are to use beta-sheet torsions. amino-isomer: Variable, Read/Write.Type: enum(l, d).Whether amino acids are l or d.amino-omega: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Omega amino acid backbone angle.amino-phi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Phi amino acid backbone angle.amino-psi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Psi amino acid backbone angle.animate-vibrations: Variable, Read/Write.boolean.Type:Whether or not to animate vibrations.annotation-color: Variable, Read/Write.string.Type:Default color for annotations.annotation-filled: Variable, Read/Write.boolean.Type:The circle and rectangle annotations are filledannotation-layer-hidden: Variable, Read/Write.boolean.Type:The annotation layer is hidden andd only molecule layer shows. annotation-layer-in-front: Variable, Read/Write.boolean.Type:The annotation layer is in front of molecule layer.append-dynamics-average: Command.Arg list: string.Add a named selection to dynamics average gathering.append-dynamics-graph: Command.Arg list: string.Add a named selection to dynamics graph display.append-omsgs-to-file: Command.Arg list: string.String-1 gives the name of a file to which o-msgs are to be appended. assign-basisset: Command.Arg list: string.Assign a basis set to a selection or system.atom-basisset: Variable, Read/Write.Type: array of string.(iat, imol) The basis set of atom iat in molecule imol.atom-charge: Variable, Read/Write.(iat, imol) The charge of atom iat in molecule imol.atom-color: Variable, Read/Write.Type: array of enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).(iat, imol) The current color of the atom.atom-count: Variable, Readonly.Type: vector of integer.(imol) The number of atoms in molecule imol.atom-extra-basisset: Variable, Read/Write.Type: array of string, float.(iat, imol) The basis set of atom iat in molecule imol.atom-info: Variable, Readonly.(unknown).Type:Funny composite to support backends.atom-label-text: Variable, Readonly.Type: array of string.(iat, imol) RO. The text of the current atom label.atom-labels: Variable, Read/Write.Type: enum(None, Symbol, Name, Number, Type, Charge, Spin, Mass, BasisSet, Chirality, RMSGradient, Custom).Label for atoms.atom-mass: Variable, Read/Write.Type: array of float.(iat, imol) The mass of atom iat in molecule imol.atom-name: Variable, Read/Write.Type: array of string.(iat, imol) The name of atom iat in molecule imol.atom-spin-density-at-nucleus: Variable, Read/Write.Type: array of float.(iat, imol) The electron density of nucleus of atom iat in molecule imol.atom-spin-population: Variable, Read/Write.Type: array of float.(iat, imol) The spin density of atom iat in molecule imol.atom-type: Variable, Read/Write.Type: array of string.(iat, imol) The type of atom iat in molecule imol.atomic-number: Variable, Read/Write.(iat, imol) The atomic number of atom iat in molecule imol.atomic-symbol: Variable, Readonly.Type: array of string.(iat, imol) The element symbol of the atom.auxilliary-basis: Variable, Read/Write.Type: integer in range (0 .. 3).1=A1, 2=A2, 3=P1back-clip: Variable, Read/Write.float.Type:Set back clipping plane.backend-active: Variable, Read/Write.boolean.Type:Whether current channel is an active backend.backend-communications: Variable, Read/Write.Type: enum(Local, Remote).Whether to compute on local or remote host.backend-host-name: Variable, Read/Write.string.Type:The name of remote host for backend communications.backend-process-count: Variable, Read/Write.Type: integer in range (1 .. 32).The number of processes to run.backend-user-id: Variable, Read/Write.string.Type:The user id to use on the remote host for backend communications.backend-user-password: Variable, Read/Write.string.Type:The password for user id to use on the remote host for backend communications. balls-highlighted: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be highlighted when shaded.balls-radius-ratio: Variable, Read/Write.Type: float in range (0.001 .. 1).Size of the Balls relative to the maximum value.balls-shaded: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be shaded.basisset-count: Variable, Readonly.integer.Type:Number of coefficients required to describe a molecular orbital.bend-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.beta-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.beta-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.bond-color: Variable, Read/Write.Type: enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).The color used for drawing atoms and bonds.bond-spacing-display-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Bond spacing display ratio.builder-enforces-stereo: Variable, Read/Write.boolean.Type:Whether the model builder implicitly enforces any existing stereochemistry. calculation-method: Variable, Read/Write.Type: enum(MolecularMechanics, SemiEmpirical, AbInitio, DFT).Whether molecular mechanics, semi-empirical, or ab initio.cancel-menu: Variable, Read/Write.Type:boolean.Whether the cancel menu is up, or the normal one.cancel-notify: Command.Arg list: string.String-1 names a variable to stop watching.change-stereochem: Command.Arg list: integer, integer.Immediately change the stereochemistry about (iat, imol).change-user-menuitem: Command.Arg list: integer, string, string.Change the text and procedure associated with the specified user MenuItem. chirality: Variable, Read/Write.Type: array of string.(iat, imol) A, R, S, or ?, for achiral, R, S, or unknown chirality. ci-criterion: Variable, Read/Write.Type: enum(Energy, Orbital).One of: energy, orbital.ci-excitation-energy: Variable, Read/Write.Type: float in range (0 .. 10000).When ci-criterion=energy, maximum excitation energy.ci-occupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of occupied orbitals included. ci-state-to-optimize: Variable, Read/Write.Type: integer in range (0 .. 32767).Which CI state to optimize with conjugate directionsci-unoccupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of unoccupied orbitals included. clip-cursor: Variable, Read/Write.Type: float in range (0 .. 1000).Select Z axis clip cursor tool.clip-icon-step: Variable, Read/Write.Type: float in range (0 .. 1000).Select clip step.color-element: Command.Arg list: integer, enum().Element Int-1 gets color String-2 as its default color.color-selection: Command.Arg list: string.String-1 names a color for the current selection.compile-script-file: Command.Arg list: string, string.Compile file string-1, writing result to string-2 configuration: Variable, Read/Write.integer.Type:The current UV configuration of the system.configuration-interaction: Variable, Read/Write.Type: enum(NoCI, SinglyExcited, Microstate).One of: no-ci, singly-excited, microstate.connectivity-in-pdb-file: Variable, Read/Write.Type:boolean.Whether connectivity information is to be included in a PDB file.constrain-bond-angle: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the angle constraint for the three currently selected atoms. constrain-bond-down: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be down.constrain-bond-length: Command.Arg list: float in range (0 .. 100).Float-1 gives the length constraint for the two currently selected atoms. constrain-bond-torsion: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the torsion constraint for the four currently selected atoms. constrain-bond-up: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be up.constrain-change-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to change the current stereochemistry.constrain-drawing: Variable, Read/Write.boolean.Type:Whether to constrain bond lengths and angles to canonicalize drawing of moleculeconstrain-fix-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to enforce the current stereochemistry.constrain-geometry: Command.Arg list: string.String-1 describes the geometry constraint around the currently selected atom. coordinates: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z coordinates of atom iat in molecule imol. coordination: Variable, Readonly.Type: array of integer.(iat, imol) The coordination number for the specified atom.correlation-functional: Variable, Read/Write.Type: enum(None, Perdew86, VWN, LYP, PZ81, PW91, PBE96, HCTH98).Perdew, LYP, etc.cpk-max-double-buffer-atoms: Variable, Read/Write.Type: integer in range (0 .. 2147483647).Maximum number of double buffered atoms in cpk rendering mode. create-atom: Command.Arg list: integer in range (0 .. 103).Create a new atom at the origin with atomic number nAtno.current-file-name: Variable, Readonly.string.Type:The name of the current file.custom-title: Variable, Read/Write.string.Type:Custom Title string, append string to title.cutoff-inner-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) to begin a switched cutoff.cutoff-outer-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) at which nonbonded interactions become zero. cutoff-type: Variable, Read/Write.Type: enum(None, Switched, Shifted).Electrostatic cutoff to apply to molecular mechanics calculations.cycle-atom-stereo: Command.Arg list: integer, integer.Advance the stereo constraint about atom (iat, imol).cycle-bond-stereo: Command.Arg list: integer, integer, integer, integer.Advance the stereo constraint along the bond (iat1, imol1)--(iat2, imol2). cylinders-color-by-element: Variable, Read/Write.boolean.Type:Color Cylinders using element colors.cylinders-width-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Width of the Cylinders relative to the maximum value.d-orbitals-on-second-row: Variable, Read/Write.Type:boolean.Include D orbitals on second row.declare-float: Command.Arg list: string.Declare a new floating-point variable.declare-integer: Command.Arg list: string.Declare a new integer variable.declare-string: Command.Arg list: string.Declare a new string variable.default-element: Variable, Read/Write.Type: integer in range (0 .. 103).The atomic number of the default element for drawing operations. delete-atom: Command.Arg list: integer, integer.Delete the specified atom.delete-file: Command.Arg list: string.filename to be deleted.delete-named-selection: Command.Arg list: string.Remove the named selection String-1 from the list of named selections. delete-selected-atoms: Command.Arg list: (void).Delete the currently selected atoms.dipole-moment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Dipolemoment.dipole-moment-components: Variable, Read/Write.Type: float, float, float.Dipole moment components.do-langevin-dynamics: Command.Arg list: (void).Perform a Langevin dynamics computation on the system.do-molecular-dynamics: Command.Arg list: (void).Perform a molecular dynamics computation on the system.do-monte-carlo: Command.Arg list: (void).Perform a Monte Carlo computation on the system.do-optimization: Command.Arg list: (void).Perform a structure optimization on the system.do-qm-calculation: Variable, Read/Write.boolean.Type:For single-point QM calculations, whether to re-compute wave function. do-qm-graph: Variable, Read/Write.boolean.Type:For single-point QM calculations, to graph some data.do-qm-isosurface: Variable, Read/Write.boolean.Type:For single-point QM calculations, to generate iso-surface of results.do-single-point: Command.Arg list: (void).Perform a single-point computation on the system.do-vibrational-analysis: Command.Arg list: (void).Perform a vibrational analysis computation on the system.dot-surface-angle: Variable, Read/Write.Type: float angle in range (-90 .. 90).Dot surface angle.double-buffered-display: Variable, Read/Write.boolean.Type:Whether display operations are double-buffered.dynamics-average-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Computation results from dynamics run.dynamics-bath-relaxation-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Bath relaxation time for dynamics.dynamics-collection-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics data collection interval.dynamics-constant-temp: Variable, Read/Write.boolean.Type:Whether to keep temperature fixed at dynamics-simulation-temp. dynamics-cool-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-simulation-temp to dynamics-final-temp. dynamics-final-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Temperature to cool back to when annealing.dynamics-friction-coefficient: Variable, Read/Write.Type: float in range (0 .. 1000000).Friction coefficient for Langevin dynamics.dynamics-heat-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-starting-temp ->dynamics-simulation-temp.dynamics-info-elapsed-time: Variable, Readonly.Type: float in range (0 .. 1e+010).Elapsed time in dynamics run.dynamics-info-kinetic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-last-update: Variable, Readonly.boolean.Type:Last update from dynamics run.dynamics-info-potential-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-temperature: Variable, Readonly.Type: float in range (0 .. 1e+010).Computation results from dynamics run.dynamics-info-total-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-playback: Variable, Read/Write.Type: enum(none, playback, record).Playback a recorded dynamics run.dynamics-playback-end: Variable, Read/Write.Type: integer in range (0 .. 32767).End playback of recorded dynamics run.dynamics-playback-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics playback interval.dynamics-playback-start: Variable, Read/Write.Type: integer in range (0 .. 32767).Start playback of recorded dynamics run.dynamics-restart: Variable, Read/Write.boolean.Type:Use saved velocities.dynamics-run-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Total integration time at dynamics-simulation-temp. dynamics-seed: Variable, Read/Write.Type: integer in range (-32768 .. 32767).Seed for dynamics initialization random number generator. dynamics-simulation-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).High temperature for the dynamics run.dynamics-snapshot-filename: Variable, Read/Write.string.Type:Name file of to store dynamics run.dynamics-snapshot-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Set recording interval of dynamics run.dynamics-starting-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Starting temperature for the dynamics run.dynamics-temp-step: Variable, Read/Write.Type: float in range (0 .. 1e+010).Step size (K) by which temperature is changed.error: Variable, Read/Write.string.Type:The current error.errors-are-not-omsgs: Command.Arg list: (void).Specifies that error messages are to appear in message boxes. errors-are-omsgs: Command.Arg list: (void).Specifies that error messages should be treated like o-msgs. estatic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.exchange-functional: Variable, Read/Write.Type: enum(None, Hartree-Fock, Slater, Becke88, PW91, Gill96, PBE96, HCTH98, B3-LYP, B3-PW91, EDF1, Becke97).Slater, Becke88, etc.excited-state: Variable, Read/Write.boolean.Type:False for lowest state, true for next-lowest state.execute-client: Command.Arg list: string.Run a client application.execute-hyperchem-client: Command.Arg list: string.Run a client application. App can reliably connect to instance of HyperChem. execute-string: Command.Arg list: string.Execute the string variable as a script.exit-script: Command.Arg list: (void).Exit the current script.explicit-hydrogens: Variable, Read/Write.boolean.Type:Whether hydrogens are to be drawn explicitly.export-dipole: Variable, Read/Write.boolean.Type:Whether or not to export dipole moment data to .EXT file.export-ir: Variable, Read/Write.boolean.Type:Whether or not to export IR data to .EXT file.export-orbitals: Variable, Read/Write.boolean.Type:Whether or not to export orbital data to .EXT file.export-property-file: Command.Arg list: string.Writes properties to the named file.export-uv: Variable, Read/Write.boolean.Type:Whether or not to export UV data to .EXT file.factory-settings: Command.Arg list: (void).Reset chem to its out-of-the-box state.field-direction: Variable, Read/Write.Type: integer in range (1 .. 3).direction (X,Y or Z) of the static electric field applied to the systemfield-strength: Variable, Read/Write.Type: float in range (-1000 .. 1000).strength (a.u.) of the static electric field applied to the systemfile-diff-message: Command.Arg list: string, string, string, string.Compare file1 to file2; if they are the same say string3, else say string4.file-format: Variable, Read/Write.string.Type:The molecule file format.file-needs-saved: Variable, Read/Write.Type:boolean.Whether the current system needs to be saved.formal-charge: Variable, Read/Write.Type: array of integer.(iat, imol) Positive or negative formal charge on atom used by model builder. front-clip: Variable, Read/Write.float.Type:Set front clipping plane.global-inhibit-redisplay: Variable, Readonly.Type:boolean.Whether redisplay of the system is inhibited (readonly)gradient-x: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the X directiongradient-y: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Y directiongradient-z: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Z directiongradients: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z gradients of atom iat in molecule imol.graph-beta: Variable, Read/Write.boolean.Type:If true and UHF, graph beta-spin orbitals instead of alpha.graph-contour-increment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Increment between contour lines.graph-contour-increment-other: Variable, Read/Write.boolean.Type:Whether to use graph-increment-other (true) or use defaults (false).graph-contour-levels: Variable, Read/Write.Type: integer in range (1 .. 32767).The number of contour levels to plot.graph-contour-start: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Value for first contour line.graph-contour-start-other: Variable, Read/Write.boolean.Type:Whether to use graph-contour-start (true) or use defaults (false).graph-data-row: Variable, Readonly.Type: vector of float-list.(i) The values on the i-th row of graph data.graph-data-type: Variable, Read/Write.Type: enum(electrostatic, charge-density, orbital, orbital-squared, spin-density).The type of wavefunction data to plot.graph-horizontal-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the horizontal direction.graph-orbital-offset: Variable, Read/Write.Type: integer in range (0 .. +Inf).Display orbital offset.graph-orbital-selection-type: Variable, Read/Write.Type: enum(lumo-plus, homo-minus, orbital-number).Display orbital type.graph-plane-offset: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Offset along viewer's Z axis of the plane of the data to plot.graph-vertical-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the vertical direction.grid-max-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface maximum grid value.grid-min-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface minimum grid value.hbond-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.heat-of-formation: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Heat of formation.help: Command.Arg list: string.Give help on topic String-1.hide-errors: Variable, Read/Write.boolean.Type:Whether to display error messages on the screen (channel specific). hide-messages: Variable, Read/Write.boolean.Type:Whether to display MESSAGE value on the screen.hide-toolbar: Variable, Read/Write.boolean.Type:Command to toggle the toolbar.hide-warnings: Variable, Read/Write.boolean.Type:Whether to display warning messages on the screen (channel specific). huckel-constant: Variable, Read/Write.Type: float in range (0 .. 10).Extended Huckel constant.huckel-scaling-factor: Variable, Read/Write.Type: float in range (0 .. 100000).Extended Huckel scaling factor.huckel-weighted: Variable, Read/Write.boolean.Type:Extended Huckel weighting factor.。