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CAChe Frequently Asked Questions
Q. What's new in CAChe?
A. For what's new for Macintosh click here.
For what's new for Windows click here.
Q. What's the status of CAChe 5?
A. CAChe 5 has completed final testing and is in production. Evaluation downloads are available.
Q. Does CAChe run on Windows Xp?
A. We have concentrated our testing efforts for CAChe so far on Windows Me/98, NT and 2000. CAChe does run on Windows Xp, but has not yet been thoroughly tested on this platform. Within the next few months we will be carrying out a full program of testing on Windows Xp, and we will incorporate any required bug fixes in a future release of CAChe for Windows. At present, there are no known bugs specific to Windows Xp.
Q. Does CAChe run on Windows 2000?
A. Yes. CAChe has been tested and certified for Windows 2000.
Q. Does CAChe run on the AMD Athlon process?
A. We have concentrated our testing efforts for CAChe so far on Intel Pentium processors. CAChe does run on the AMD Athlon processors and many customers are using CAChe with the Athlon processor without problems. At present, there are no known bugs specific to AMD processors.
Q. What are the differences between the Macintosh and Windows versions of CAChe?
A. CAChe is designed to take full advantage of Macintosh features on the Macintosh and Windows features on Windows computers. The user interface is native to each platform and consequently the look and feel are different.
In addition, there are some differences in functionality. For example, the Macintosh has a polymer builder and reads Chem3D files. CAChe for Windows has a tool ribbon and a single Workspace that combines the Macintosh Editor and Visualizer.
CAChe 5.0 has additional differences from the Macintosh 4.5 version. CAChe 5.0 has MOPAC 2002 with atom limits to 20,000. CAChe 5.0 Pro is expanded to work with tens of thousands of atoms and has a sequence view for working with protein sequences. In also has a worksheet style workbook for viewing and manipulating chemical sample data, a new find command, select neighbor command and more.
Q. What are the molecule size limits for each application in CAChe on desktop Macs and PCs?
A. On Macs:
- Molecular Mechanics: over 1,000 atoms.
- Molecular Dynamics, which is based on the Molecular Mechanics: over 1,000 atoms.
- MOPAC 2000: up to 1,000 atoms.
- Extended Huckel (EHT) does not have discreet atom number limits, but generally can handle molecules of about the same maximum size as MOPAC.
- ZINDO: up to 200 atoms or up to 700 basis functions, whichever is smaller.
- Editor/Visualizer over 4,000 atoms.
- DGauss: up to 200 atoms or up to 2,000 basis functions.
A. On PCs:
- Molecular Mechanics: over 20,000 atoms.
- Molecular Dynamics, which is based on the Molecular Mechanics: over 20,000 atoms.
- MOPAC 2002: up to 20,000 atoms.
- Extended Huckel (EHT) does not have discreet atom number limits, but generally can handle molecules of about the same maximum size as MOPAC.
- ZINDO: up to 200 atoms or up to 700 basis functions, whichever is smaller.
- WorkSpace (PC) over 20,000 atoms.
- DGauss: up to 200 atoms or up to 2,000 basis functions.
Q. What are the molecule size limits for each CAChe application on a UNIX GroupServer?
A. On an SGI or IBM RS6000 CAChe GroupServer, CAChe calculation molecule size limits are:
- Molecular Mechanics: over 20,000 atoms.
- Molecular Dynamics, which is based on the Molecular Mechanics: over 20,000 atoms.
- MOPAC: up to 20,000 atoms.
- Extended Huckel (EHT) does not have discreet atom number limits, but generally can handle molecules of about the same maximum size as MOPAC.
- ZINDO: up to 200 atoms or up to 700 basis functions, whichever is smaller.
- DGauss: up to 200 atoms or up to 2,000 basis functions.
Q. Which elements can each application in CAChe handle?
A. Application:
- Extended Huckel (EHT):
all elements, up to Lawrencium (#103).
- MOPAC calculations can be run using several different parameterization sets, the most commonly used being AM1 and PM3.
- MOPAC 2002 PM5:
H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Ca, Zn, Ga, Ge, As, Se, Br, Rb, Sr, Cd, In, Sn, Sb, Te, I, Cs, Ba, Hg, Tl, Pb, and Bi.
- MOPAC 2000 AM1:
H, B, C, N, O, F, Al, Si, P, S, Cl, Zn, Ge, Br, I, and Hg.
- MOPAC 2000 PM3:
H, Li, Be, C, N, O, F, Mg, Al, Si, P, S, Cl, Zn, Ga, Ge, As, Se, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, and Bi.
- CAChe Augmented Molecular Mechanics and Molecular Dynamics:
all elements, up to Lawrencium (#103).
- ZINDO has separate parameterization sets for geometry optimizations/energy calculations and for UV-visible spectral calculations.
- ZINDO geometry optimizations/energy calculations:
H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Br, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, and I.
- ZINDO UV-visible spectral calculations:
H, Li, B, C, N, O, F, P, S, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn.
- DGauss:
all elements up to Radium (#88).
Q. Which file formats can be imported into and exported from CAChe?
A. Formats:
Q. Can CAChe be used for process chemistry?
A. Yes. CAChe's QM applications can be used to study the kinetics and thermodynamics of chemical reactions. CAChe has been used to study catalysis, solvent effects and temperature effects in synthetic and process chemistry.
Q. How can CAChe help with polymer chemistry?
A. CAChe ProjectLeader can determine polymer properties including polymer Tg, molar volume, cohesive energy, and the polymer solubility parameter, as well as molar refractivity. From these properties, many other polymer properties can be calculated using standard equations from texts such as Bicerano and van Krevelan.
Mac CAChe has a powerful polymer builder, for precise construction of hetero- and homo-polymers specifying head attachment angle, tail attachment angle, head bond angle, tail bond angle, center dihedral, bond length, and repeat factor.
In addition, numerous applications determining polymer properties such as thermal degradation, weatherability, and miscibility have been developed and are available.
Q. What training resources are there for CAChe?
A. CAChe field training is offered on a by-request basis. We offer a one-day course called Chemistry By Design which combines hands-on lab (computer) exercises and lectures, covering the CAChe software's capabilities and the theory behind it. The Chemistry By Design course can be provided to a group of up to 20 people ranging in experience from beginners to experienced CAChe users.
We can also provide custom designed full-day or half-day courses specifically tailored to your group's research interests and how best to use CAChe to address them.
Once per year we host the 4-day CAChe Advance Course in our Portland, Oregon office. CAChe Advance is designed for CAChe users who need to develop more advanced strategies and problem-solving methodologies to optimize the use of computer-aided chemistry in their research. Lab time is set aside to work on your specific research interests, and for you to consult with us on the best approaches to solving those problems. The high instructor to student ratio allows us to tailor the course to CAChe users of all experience levels.
Q. How does CAChe handle crystal structures?
A. CAChe has a powerful Crystal Builder interface which contains 232 space groups. You can specify the space group and unit cell parameters, and the number of times the unit cell is repeated in the crystal lattice, and can build molecules, molecular crystals, infinite lattices, or structures containing only the asymmetric atoms.
Q. What is the difference between CAChe and BioMedCAChe?
A. CAChe WorkSystem contains a Builder/Viewer, a Tabulator for rendering graphical surfaces, the ProjectLeader spreadsheet interface, and calculation applications including Molecular Mechanics, Molecular Dynamics, MOPAC, ZINDO and Extended Huckel. The WorkSystem is available for both Macintosh and Windows PCs.
BioMedCAChe contains the CAChe Builder/Viewer, Tabulator, and ProjectLeader spreadsheet interface, and Molecular Mechanics, Molecular Dynamics, MOPAC, and CONFLEX, our exhaustive automated conformation searching tool. BioMedCAChe runs on Windows PCs. BioMedCAChe also contains the Sequence View for editing and working with protein sequences.
Q. Is there a CAChe user group?
A. Yes. It is hosted by professor James Currie at Pacific University, Forest Grove Oregon, USA. To subscribe, send an email to "Majordomo@pacificu.edu" with the following command in the body of your email message:
subscribe cache
The CAChe list is intended to enhance communication between academic users of computer modeling for teaching. In particular, on applications of the CAChe molecular modeling tools in the undergraduate curriculum. Supporting files such as a syllabus, molecule structure files, or QuickTime movies will be posted to a CAChe folder on the Natural Science Gopher server located in Pacific University.
Q. How many CAChe licenses have been sold?
A. Over four thousand CAChe licenses have been sold worldwide, in North America, Japan, Europe, and the Asia-Pacific region.
Q. Are site licenses available for CAChe?
A. Yes. The Annual Academic Site License is entering its 4th year and is used at nearly 50 colleges and universities nationwide including Stanford University, the University of Michigan, Swarthmore College and Grinnell College among others.
Industrial Site Licenses and Group-Wide Licenses are also available.
Q. What is the largest molecule that can be displayed in CAChe?
A. Molecules of at least 2,000 atoms (Mac) and more than 20,000 atoms (PC) can be viewed, moved, and rotated to be viewed from any angle in CAChe.
Q. What optional add-ons are available for CAChe?
A. Two optional computational modules, DGauss and CONFLEX are available to be added onto any CAChe product. DGauss, our Density Functional Theory (DFT) module runs on WindowsNT and UNIX (SGI or IBM RS6000) CAChe GroupServer. CONFLEX, an exhaustive, systematic conformational searching algorithm developed by Dr. H. Goto, runs on desktop Mac & Windows platforms and on CAChe GroupServer (SGI or IBM RS6000).
Q. What stereoscopic display options are available for CAChe?
A. A 3D stereo option for CAChe is currently available for WindowsNT. CAChe stereo uses an OpenGL software format, and 3rd party monitors, stereo shutters (NuVision, Stereographics) and 3D video cards (3DLabs). Currently no 3D stereo hardware is available for the Mac.
Q. Can CAChe run calculations remotely in a client-server architecture?
A. Yes. CAChe calculations using any of the CAChe computational applications (Molecular Mechanics, Molecular Dynamics, MOPAC, ZINDO, EHT, Tabulator, CONFLEX, and DGauss) can be set up and launched from a desktop Mac or PC to run on a local or remote UNIX CAChe GroupServer (SGI or IBM RS6000). The results are returned automatically to the client Mac or PC to be viewed. The Client/Server architecture is completely transparent to the user; once installed, the user need not know anything about UNIX or networking to access the GroupServer for calculations.
Q.What properties can be calculated by CAChe?
A. CAChe can calculate many properties of molecules, atoms, molecular orbitals, spectra, and molecular conformation. Some examples are:
- Molecular properties:
- heat of formation
- dipole moment
- HOMO and LUMO energy
- ionization potential
- polarizability
- lambda max UV-visible
- IR spectra
- logP
- polymer Tg
- free energy
- transition states & activation energy
- nucleophilicity & electrophilicity
- bond lengths
- non-bonded atom distances
- bond angles & dihedral angles
- bond orders & bond strain
- volume and surface area
- dynamic reaction coordinates
- Atomic properties:
- HOMO & LUMO densities
- partial charges
- electrophilic, radical, & nucleophilic susceptibilities
- superdelocalizabilities
- CAChe can also create and graphically render:
- electron density isosurfaces
- molecular orbitals
- electrostatic potential surfaces
- nucleophilicity & electrophilicity reactivity surfaces
- superdelocalizability surfaces
With CAChe's conformational searching tools, you can determine local and global energy minima, structures of conformers close in energy to the lowest energy structure, and potential energy maps and surfaces.
Q. How can CAChe be used to predict other properties e.g. environmental fate or octanol-saline partition coefficient?
A. CAChe directly calculates structure, energy, and electronic structure of molecules, providing properties such as heat of formation, dipole moment, HOMO energy, partial atomic charges, wavelengths of UV-visible absorption, etc.
Using CAChe's ProjectLeader spreadsheet interface to develop a Quantitative Structure Property Relationship (QSPR), you can correlate computer-calculated results to any measurable property of interest. This allows you to predict properties such as boiling point, toxicity, catalytic activity, acidity & basicity, antibacterial activity, vapor pressure, water solubility, reaction rate constants and many others.
Using QSPR, you can predict values for your property of interest for compounds lacking experimental data, even for compounds which have never been synthesized.
Q. How does Molecular Mechanics represent and handle hydrogen bonds?
A. MM2 includes Hydrogen Bond interactions "automatically" by recognizing the nonbonded interactions between certain atom pairs as hydrogen hydrogen bonds. Special parameters are assigned to the interactions of these atom pairs (to distinguish them from ordinary van der Waals type of nonbonded interactions). Therefore, it is usually not necessary to explicitly represent hydrogen bonds. You may also verify that the particular atom pairs are classified as hydrogen bonds by examining the "Molecular Mechanics Details" file, where all the hydrogen bonded atoms are listed.
Q. How can I get additional copies of CAChe documentation?
A. CAChe User Guides and Quick Start manuals ship as Adobe Acrobat PDF files on the CAChe CD and are installed on your hard drive when CAChe is installed. You can read the manuals with Acrobat and print additional copies as needed. If you prefer printed and bound hardcopies, please contact CAChe Group sales to order additional copies.
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