I was trying to submit a QM/MM job to ADF and I wanted to use pdb2adf utility in ADF, in order to make the proper input file, but somehow was not getting it right.
I will be submitting a QM/MM job for a big cluster of molecules, with 2 molecules in the centre of the cluster treated with Quantum mechanics and surrounding 25-30 molecules treated with Molecular mechanics.
Hasi: QM, quantum mechanics; MM, molecular mechanics; ADF, molecular modeling software.
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12-05-2015 · Table of Contents. Overview. Setting up your Environment to run ADF. Submitting ADF jobs on a Research Computing Server. Tutorials. Links. Additional Help
Hasi: Molecular mechanics (MM) and quantum mechanics (QM) are two concepts for describing the concepts of matter (its structure, dynamics and energy). Both MM and QM assume the validity of the atomic theory of matter. MM treats atoms as elastic balls and atomic bonds as (un)breakable springs and non-bonded interactions via additive van der Waals and Coulombic potentials and each atom carries a partial charge (usually) placed at the center of the atom. The partial atomic charges are usually derived from ab initio QM calculations; hence MM is to some extent dependent on the validity of the QM concept; isn't that somewhat paradoxical? (Yes, it is.) QM treats atoms --- well, nobody knows what QM is, because nobody understands it --- as having electrons, the magic particles/waves that exist in atomic orbitals; except that electrons (some think and I feel that they might be right) do not exist and even if we assume that electrons do exist, they certainly do not orbit anything.
The MM concept fails in the "sub-atomic" world; QM fails in the
"(supra)macromolecular" world (and beyond). Obviously, the two concepts are fundamentally wrong, because the underlying principle of all natural phenomena, regardless of scale (from "atom" to "planet" to "universe") must be one and only one. Combining the two concepts into "QM/MM" hybrid in which one treats the "important" region of the system using the QM concept and the rest using the MM concept is quite popular. And what is popular is usually wrong; sometimes very wrong.
Basuroy,
The easiest way to prepare your molecule is that, download .mol files for individual molecules of your complex and then put them in same file so as now your complex will be ready in single file. Now you save the structure as a gaussian input file (.gjf). Now you can run the gaussian job in suitable method. Hope it helps.
Sorry for not seeing this earlier. We do not see all ResearchGate questions.
You could contact the ADF mailing list or our support team in the future. Here's an example on how to set up QM/MM calculations from a pdb:
https://www.scm.com/doc/QMMM/pdb2adf/pdb2adf.html
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