Dear all,
I made a semiempirical orbital calculation (using MOPAC) of a fairly large complex of a ligand and a protein binding site. Now I am trying to find the highest occupied orbital with a large (the largest) contribution of the catalytic residue (oxygen of a serine in this case) as well as the lowest unoccupied orbital with a large contribution of the reactive atom (carbonyl carbon) within the ligand.
The output contains a total of roughly 2000 molecular orbitals. Does anyone have suggestions of a piece of software that could help me here?
Thanks in advance
I suggest you use xtb code (https://github.com/grimme-lab/xtb/) instead of MOPAC to perform the calculation of your complex. The GFN2-xTB implemented in xtb is generally more robust than all available semiempirical methods. More importantly, if you add "--molden" argument in xtb, then xtb will produce .molden file, which can be used as wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). In Multiwfn, main function 0 is able to visualize orbitals (see Section 4.0 of Multiwfn manual for detail), and Multiwfn has a powerful orbital composition analysis module, which can easily examine contribution of various atoms or user-defined fragment to different orbitals, see Section 4.8 of the manual for examples.
You can try the gabedit program, this software have a tool to read/visualize the molecular orbitals of Mopac output files ...
Thank you for the hint Jose-Zeferino Ramirez Ramirez
Unfortunately gabedit hangs/crashes when it tries to load the orbital information from the MOPAC aux file.
I suggest you use xtb code (https://github.com/grimme-lab/xtb/) instead of MOPAC to perform the calculation of your complex. The GFN2-xTB implemented in xtb is generally more robust than all available semiempirical methods. More importantly, if you add "--molden" argument in xtb, then xtb will produce .molden file, which can be used as wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). In Multiwfn, main function 0 is able to visualize orbitals (see Section 4.0 of Multiwfn manual for detail), and Multiwfn has a powerful orbital composition analysis module, which can easily examine contribution of various atoms or user-defined fragment to different orbitals, see Section 4.8 of the manual for examples.
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