Citation & Funding

Garleek is scientific software, funded by public research grants: Spanish MINECO (project CTQ2017-87889-P, CTQ2017-87792‐R, Severo Ochoa Excellence Accreditation 2014–2018 SEV‐2013‐0319), Generalitat de Catalunya (project 2014SGR989, CERCA Programme); J.R.-G.P.: Generalitat de Catalunya (grant 2017FI_B2_00168); I.F.-A.: Spanish MINECO (Severo Ochoa predoctoral training fellowship SVP‐2014–068662). If you make use of Garleek in scientific publications, please link back to this repository (a publication is under preparation). It will help measure the impact of our research and future funding!

Help & Support

If you have any question, doubt or suggestion, please submit an issue in our GitHub repository.

Frequently Asked Questions

Where can I find Gaussian’s documentation for external keyword?

Follow these links: Gaussian v16, v09D, v09B, v03

Why don’t you support more MM software?

Please, follow the ongoing discussion in this issue. PRs are welcome!

Does Garleek support electronic embedding?

Yes, as of v0.3, Garleek supports electronic embedding if you use the EmbedCharge option in the ONIOM keyword of the Gaussian input file. Differences in the EIn files are handled automatically.

Common Garleek/Gaussian/Tinker errors

Garleek only provides a light wrapper around Gaussian’s external keyword, so it still uses Gaussian’s ONIOM implementation, which can be a bit picky depending on the requested operations. MM is tricky itself if the parameters are not available. The list below provides some common errors we have found in our ONIOM journey. It’s not meant to be exhaustive, but a collection of the results of long debugging sessions.

Gaussian complains about basis sets not being available

Even though the MM calculation needs no basis sets, Gaussian still runs l301 on the MM part, which is responsible for preparation tasks like basis sets reading. If your system contains exotic elements (say, Rhenium or Osmium) and you are already using genecp, it won’t find compatible basis sets. The solution is to provide the basis sets manually by appending the gen option to the external call and appending two additional basis sets sections (but no pseudopotentials!) around the original basis set section corresponding to the QM genecp basis sets. Since this task is repetitive and prone to error, Garleek will do it for you. If gen or genecp options are present in the ONIOM() call, the external option will be patched with the gen keyword and the basis sets section will be amended as needed. Similarly, if the basis set is globally specified directly in the ONIOM() call (no genecp nor gen keywords, but a specific basis set like 6-31G*), it will be added to the external option just in case. When this patch is applied, you will get an informative message in the output. See tests/data/Os/ for an example input file what will benefit from this correction.

Gaussian says “MOMM, but no IMMCRS”

opt=nomicro is almost compulsoryin optimization jobs. Garleek will try to add it automatically if it’s not present, but it might fail in some cases. Please check the option is there in the route section.

Garleek-prepare says “KeyError: 75 not found in line XXXXX”

The atom type XX is not listed in the provided --types file. Due to Garleek fallback strategies, XX can be the atom type label (ie, C-XX 0.000 1.000 2.000 in the cartesian geometry specification) or the atomic number corresponding to that element.

This --types file must list atom type correspondences between the originally present atom type labels in the Gaussian input and the atom types Tinker is expecting. This way, garleek-prepare can replace them in the file and provide the Tinker ones in the patched file. If you are using custom residues, you must make sure the Tinker atom type and its parameters is correctly defined in the PRM or KEY file (specified as the --ff flag).

Tinker says “Unusual number of connected atoms”

The atom type specified for that atom center does not expect covalently bonded species and is missing the bond parameters. You can either (a) provide those parameters or (b) delete the involved bonds in the connectivity section (by hand or in GaussView).