Frequently Asked Questions:
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A shortcut to FAQs about AOMix-CDA
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If you have a question about the software and you cannot find an answer for it in the program manual and this website, please e-mail your question to S. Gorelsky. If the question is of general interest, the answer will be posted on this page (instead of an e-mail message reply to you).
Q: I use a non-English version (for example: Japanese, Chinese, or Korean) of Windows 2000 / XP. What should I do to run the programs on my computer?
Before starting the program, switch your computer to the US keyboard (type the command US in the Windows command prompt).
Q: Our group/institution has purchased the AOMix license. Will it be possible to organize the AOMix software workshop at our site?
Yes, it will be possible to have a local AOMix software workshop. Please contact the author for scheduling and other relevant details.
Q: Does AOMix use any network connectivity?
AOMix does not use any network connectivity. AOMix and its AOMix-x modules are designed to be completely clean - the program does not modify the Register in MS Windows. This is because AOMix is intended for use in a wide range of environments including those that are sensitive about security.
Q: What we want to do with AOMix is to construct a molecular orbital interaction diagram from its constituent fragments. For example using Gaussian 03 we have calculated the molecular orbitals of a metal-bisphosphine fragment, an acetonitrile fragment and the metal-bisphosphine-acetonitrile complex. What programs do we need to accomplish this task?
For the construction of the MO interaction diagrams from Gaussian 03 calculations, you will only need AOMix and AOMix-CDA.
Q: Can SWizard, AOMix and its modules be combined with output files produced by Linux versions of Gaussian 98, GAMESS, etc.?
All the programs on this website will work with output files no matter which was the original operating system. For example, I run my computational jobs on a PC Linux cluster and I run AOMix on my laptop computer under Windows XP.
Q: When I tried to run the software, I have received the "ERROR 200" message. What should I do?
In both UNIX and DOS, there are non-printing ASCII characters at the end of each line, that tell a text display program that the following text should be displayed on a new line. UNIX uses the Linefeed character to denote the end of a line. DOS uses the Carriage Return followed by the Linefeed character to denote a new line. As a consequence, UNIX text files won't display properly in most DOS/Windows text editors, and DOS text files don't display properly in UNIX text editors. If you run AOMix or SWizard on UNIX ASCII-formatted output files, you will receive the appropriate error message (error 200). There are ways to get around this problem:
Q: Do you offer an evaluation / trial version of the AOMix package?
No, I do not offer a trial version of the AOMix software. However, if you are not sure, I can only recommend that you order a cheapest single-workstation license for yourself to see how the program works.
Q: Are these programs distributed by QCPE?
No. There are two main reasons for it. First, AOMix is a DYNAMIC project. Many new features are added to the software every year. It would be hard to keep the AOMix program development by using such a STATIC thing as the QCPE software distribution system. Second, in the recent years, the Quantum Chemistry Program Exchange project is in a rather bad shape and the QCPE software distribution system and the QCPE catalog has not been updated for a while. Hopefully, things will get better in future.
Q: What is a "MAC address"?
Q: What if my computer has several network cards?
This is not a problem. Each network card has its own MAC address. The software will automatically detect all network cards and will use the registered MAC address (the one you specified in the license agreement form), ignoring the MAC addresses of all other network adapters.
Q: I have a single-user license and recently I've got a new computer and want to transfer my license to the new computer. What should I do?
fill the license transfer form.
Q: I have output files from a quantum-chemical software which currently is not included in the AOMix supported software list. What should I do?
Please collect four output files from your quantum-chemical software package:
these files should contain the LCAO-MO coefficients and, if it is a HF or DFT calculation, the overlap matrix. Please create a zip or rar file containing these four output files, also please include corresponding input files.
Q: What if I have a problem running the software?
The software has many built-in error checks. If you encounter a problem, please
If you have tried to run your calculation with the most recent version and still have a problem, please send an e-mail (software@sg-chem.net) with a description of your problem. In your e-mail, indicate
C:\AOMix\> dir > folder-list.txt
Q: What should I do to visualize the Mayer bond orders (calculated by using AOMix-L) in UCSF Chimera?
Follow these steps:
You can edit the AOMix-L-atom-chimera2.txt file before importing its data to Chimera to suit your needs:
Use the PSEUDOBONDS keyword in aomixpar.txt to change the default print format, threshold value and color for PseudoBond attribute files.
You can change atomic/background colors and atomic and bond rendering by using the standard Chimera commands. Please refer to the UCSF Chimera manual for further instructions.
AOMix-CDA
Q: How much time does it take to run an AOMix-CDA calculation for a molecule containing 50 atoms?
Approximately 5 minutes on any modern destop or laptop computer. All CPU-intensive modules of AOMix are written in Fortran for fast execution. Here are a few examples (using a laptop computer with a Pentium IV mobile 1.7 GHz processor, 256MB RAM and MS Windows XP as an operating system):
Spin-restricted calculations will take less time than spin-unrestricted calculations.
Q: I am interested to evaluate back-donation in Pt-CO clusters. Can AOMix-CDA program provide occupation numbers for 2pi* orbitals of the CO ligands in the clusters?
yes, AOMix-CDA prints occupation numbers of fragment molecular orbitals, such as 2pi* orbitals of the CO ligands in the Pt-CO clusters. Thus, you can use AOMix-CDA for the analysis of the back-donation in the Pt-CO clusters.
Q: Does the AOMix-CDA program work with applied external field in Gaussian (e.g., "FIELD" or "CHARGE" keywords)? For example, the orbital interaction diagrams?
yes, AOMix-CDA can process calculations with applied external field. This includes orbital interaction diagram calculations.
Q: In one of the AOMix-CDA jobs, we are getting a small but negative backdonation. Does it constitute a red flag meaning something is procedurally wrong? I believe I've actually seen a couple of examples from Frenking where he had a negative backdonations (BH3-NH3 off the top of my head). If it's ok, what is the physical meaning of the negative sign?
yes, negative electron donation and backdonation numbers (they are usually small and do not exceed -0.02) do come up from time to time, especially if the basis set with duffuse functions is employed in calculations. These negative values are artifacts of the Mulliken population analysis and have, of course, no physical meaning. It is safe to assume that those numbers are just zeros.
Q: I have two different molecules, one of them is X and the other one is X with a gold cluster attached to it. I want to calculate the overlap of molecular orbitals which belong to these two different molecules. The idea is to pick up the orbitals which resemble the most. For example, if I pick up orbital number 47 from the first gaussian output, I wanna calculate the overlap of this orbital with all the orbitals from the second gaussian output. Can I do this with your program?
yes, AOMix-CDA can map molecular orbitals of molecule X with molecular orbitals of complex XY. The overlap between the molecular orbital #47 of X and the molecular orbital #N of XY will be equal to a percentage contribution (devided by 100%) from orbital #47 of molecule X to the molecular orbital #N. This information is available from a standard AOMix-CDA output file.
Q: I have done some calculations on metal-olefin complexes with Gaussian03W program using the LANL2DZ basis set for the metal and 6-31G(d) for the rest of the atoms but when I tried to run AOMix-CDA I get the ERROR 5 message. On the other hand if I use the same basis set for all atoms the AOMix-CDA terminates normally. Is there a way to run AOMix-CDA using mixed basis sets?
AOMix-CDA can process calculations with mixed basis sets (the GEN keyword in Gaussian) but you need to ensure that the number of d orbitals in each shell (five vs. six) remains the same in the whole molecule and fragment calculations. In Gaussian, this can be done by using the 5D keyword for calculations with five d functions (pure d functions) and the the 6D keyword for calculations with six d functions (Cartesian d functions) per shell. When using the Gen keyword, the basis set explicitly specified in the route section always determines the default form of the basis functions.
Doing back to your example, the 6-31G(d) basis set uses Cartesian d functions by default. The LANL2DZ basis set uses pure d functions by default. If you use a mixed basis set such as LANL2DZ for metal and 6-31G(d) for the rest of the atoms, Gaussian will run a whole molecule calculation using pure d functions. If you forget to include the 5D keyword for the olefin fragment, this fragment calculation will be done using Cartesian d orbitals. Thus, the number of orbitals in the whole molecule will be less than the sum of the numbers of fragment orbitals and AOMIx-CDA will terminate giving you the ERROR 5 message.
The following example shows how to setup Gaussian calculations for the AOMix-CDA analysis of the Fe(CO)4(C2H4) complex (with Fe(CO)4 and C2H4 as fragments) when using a mixed TZVP/6-31G(d) basis set (TZVP for Fe and 6-31G(d) for the other atoms) with pure d functions:
-------- the input file for the Fe(CO)4(C2H4) ------- #P B3LYP/GEN 5D SCF=Tight Pop=Full IOp(3/33=1) The Fe(CO)4(C2H4) complex, the molecule is in standard orientation (NOSYMM is not needed) 0 1 Fe 0.000000 0.000000 0.018179 C 1.821462 0.000000 0.090291 C -1.821462 0.000000 0.090291 C 0.000000 1.503897 -0.976361 C 0.000000 -1.503897 -0.976361 O 0.000000 2.460510 -1.620978 O 0.000000 -2.460510 -1.620978 O -2.968878 0.000000 0.160975 O 2.968878 0.000000 0.160975 C 0.000000 -0.704147 2.039071 C 0.000000 0.704147 2.039071 H 0.910796 -1.252234 2.262845 H 0.910796 1.252234 2.262845 H -0.910796 1.252234 2.262845 H -0.910796 -1.252234 2.262845 Fe 0 TZVP **** O C H 0 6-31G(d) **** ----- the input file for Fragment 1 ----- #P B3LYP/GEN 5D SCF=Tight Pop=Full IOp(3/33=1) NOSYMM Fragment 1, Fe(CO)4 0 1 Fe 0.000000 0.000000 0.018179 C 1.821462 0.000000 0.090291 C -1.821462 0.000000 0.090291 C 0.000000 1.503897 -0.976361 C 0.000000 -1.503897 -0.976361 O 0.000000 2.460510 -1.620978 O 0.000000 -2.460510 -1.620978 O -2.968878 0.000000 0.160975 O 2.968878 0.000000 0.160975 Fe 0 TZVP **** O C 0 6-31G(d) **** ----- the input file for Fragment 2 ----- #P B3LYP/6-31G(d) 5D SCF=Tight Pop=Full IOp(3/33=1) NOSYMM Fragment 2, C2H4 0 1 C 0.000000 -0.704147 2.039071 C 0.000000 0.704147 2.039071 H 0.910796 -1.252234 2.262845 H 0.910796 1.252234 2.262845 H -0.910796 1.252234 2.262845 H -0.910796 -1.252234 2.262845
