ORCA: A Versatile Tool for Quantum Chemistry ORCA is a flexible, efficient, and user-friendly general-purpose tool for quantum chemistry, specifically designed with a focus on the spectroscopic properties of open-shell molecules [1]. ORCA encompasses a broad range of standard quantum chemical methods, including semiempirical approaches, Density Functional Theory (DFT), and single- and multi-reference correlated ab initio methods. The software also supports the treatment of environmental and relativistic effects. 1. Useful Resources· ORCA Forum: https://orcaforum.kofo.mpg.de/app.php/portal · FACCTS: https://www.faccts.de/ · ORCA Tutorials: https://www.orcasoftware.de/tutorials_orca/index.html 2. Installation (Optimized for ORCA 6.1.0)2.1 Easy Linux Installation (Single User)2.1.1 Download the installer to ~/Downloads/:cd ~/Downloads wget <ORCA_6.1.0_installer>.run
2.1.2 Make it executable and run it:chmod a+x orca_6_1_0_linux_x86-64_shared_openmpi418.run ./orca_6_1_0_linux_x86-64_shared_openmpi418.run
2.1.3 Update your ~/.bashrc (the installer does this automatically):export PATH=~/orca_6_1_0:$PATH
2.1.4 Launch ORCA simply with orca, or for MPI jobs:~/orca_6_1_0/orca input.inp > output.out
2.2 Manual Linux Installation (Multi‑User, Ubuntu)2.2.1 Prepare /opt/sudo su cd /opt
2.2.2 Extract ORCAtar xvf /path/to/orca_6_1_0_linux_x86-64_shared_openmpi418.tar.xz mv orca_6_1_0_linux_x86-64_shared_openmpi418 orca_6_1_0
2.2.3 Create and Assign Groupgroupadd -g 2222 orca usermod -aG orca <your_user> chown -R root:2222 /opt/orca_6_1_0 chmod -R 750 /opt/orca_6_1_0
2.2.4 Install Compilerapt update apt install -y gcc build-essential
2.2.5 Install OpenMPIcd /opt wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.8.tar.gz tar xvf openmpi-4.1.8.tar.gz cd openmpi-4.1.8 ./configure --prefix=/opt/.openmpi make all install chown -R root:2222 /opt/openmpi-4.1.8 chmod -R 750 /opt/openmpi-4.1.8
2.2.6 Update User Environmentsu <your_user> cat << 'EOF' >> ~/.bashrc # ORCA 6.1.0 export PATH=/opt/orca_6_1_0:$PATH export LD_LIBRARY_PATH=/opt/orca_6_1_0:$LD_LIBRARY_PATH export PATH=/opt/.openmpi/bin:$PATH export LD_LIBRARY_PATH=/opt/.openmpi/lib:$LD_LIBRARY_PATH alias orca="/opt/orca_6_1_0/orca" EOF source ~/.bashrc
2.3 Installing the xTB Module2.3.1 Download v6.7.1:cd ~/Downloads wget https://github.com/grimme-lab/xtb/releases/download/v6.7.1/xtb-6.7.1-linux-x86_64.tar.xz
2.3.2 Extract:tar -xf xtb-6.7.1-linux-x86_64.tar.xz
2.3.3 Install:sudo cp xtb-dist/bin/xtb /opt/orca_6_1_0/ /opt/orca_6_1_0/xtb –version
2.3.4 macOS InstallationDownload the macOS package from the ORCA Forum and follow the Linux instructions, adjusting paths accordingly. 2.4 Windows InstallationRefer to the ORCA manual for the latest Windows support information.
3. Calculating RESP Charges Using ORCA and MultiwfnThis section provides a step-by-step guide to calculate RESP (Restrained Electrostatic Potential) charges using ORCA and Multiwfn [2]. 3.1 Generating a Molden Input FileRESP charge calculation requires a Molden-format file from your ORCA calculation. To generate this file, Navigate to the directory containing your ORCA calculation files and run the following commands: orca_2mkl job -molden mv job.molden.input job.molden · orca_2mkl: A utility provided by ORCA to convert ORCA output into various formats. · job: Replace this with the base name of your ORCA input/output files. · -molden: Specifies the generation of a Molden-format file. · mv job.molden.input job.molden: Renames the generated file for compatibility with Multiwfn. The job.molden file will now serve as input for the RESP charge calculation in Multiwfn. 3.2 Extracting RESP Charges with MultiwfnOnce the Molden file is ready, use Multiwfn to extract RESP charges. Run the following script, replacing job.molden with your file name:
Multiwfn << EOF job.molden 7 18 1 y 0 0 q EOF 3.3 Handling Missing Atom RadiiIf you encounter missing atom radii during the process, Multiwfn will prompt you to provide them. Options include: · Manually inputting radii: You can enter the missing radii based on your molecular system. · Scaling radii: Follow the instructions provided by Multiwfn to scale the radii appropriately.
3.4 Addressing Library ErrorsMultiwfn may require additional system libraries. If errors like "missing library" occur, install the dependencies using the following commands:
3.4.1 Switch to superuser mode:sudo su
3.4.2 Update the package manager:apt-get update -y
3.4.3 Install the required libraries:apt-get install -y libmotif-common libxm4 libgfortran3 · libmotif-common: A library required for GUI support in Multiwfn. · libxm4: A dependency for motif-based applications. · libgfortran3: A library for Fortran-based computations. After resolving these issues, rerun Multiwfn to complete the RESP charge fitting. 4. Extracting Force Constants from Frequency CalculationsThe orca_vib utility in ORCA allows you to extract force constants from the results of a frequency calculation. It processes the Hessian file generated by ORCA and outputs vibrational frequency data, including force constants. Procedure 4.1 Ensure that your ORCA frequency calculation has successfully completed and generated the necessary Hessian file (e.g., 2.hess).4.2 Use the following command to process the Hessian file:
orca_vib 2.hess > 2.freq · orca_vib: The ORCA utility for vibrational analysis. · 2.hess: The Hessian file generated by the frequency calculation. · 2.freq: The output file containing vibrational frequencies and force constants. Output The resulting file (2.freq) contains detailed vibrational information, including frequencies, normal modes, and the force constants for each mode. These force constants are often used in further analyses, such as molecular vibrations, thermodynamic properties, or reaction dynamics. Force constants are presented in the Approximate Stretching Force Constants section of the 2.freq file. This section shows force constants for bonds between atoms in the system and provides additional details: · Bond types (e.g., C-H, C-C, etc.). · Bond lengths (in angstroms). · Force constants (in mdyne/Ĺ). Below is an example output from the 2.freq file:
-------------------------------------- APPROXIMATE STRETCHING FORCE CONSTANTS --------------------------------------
NN FOR ATOM 0: 1 2 3 4 9 96 TYPE : C-H C-H C-C C-N C-C C-H BOND LENGTH (ANGSTROEM) : 1.1050 1.1054 1.4829 2.5602 2.5782 1.0999 FORCE CONSTANT (MDYNE/ANGSTROEM): 4.7625 4.7419 3.9918 0.4335 0.3340 4.9909
NN FOR ATOM 1: 0 2 3 96 TYPE : H-C H-H H-C H-H BOND LENGTH (ANGSTROEM) : 1.1050 1.7831 2.1578 1.7829 FORCE CONSTANT (MDYNE/ANGSTROEM): 4.7625 0.3070 0.3889 0.2796 Note: In ORCA and the 2.freq file, atom numbers start from 0 rather than 1. 4.3 Conversion of Force ConstantsThe force constants in the 2.freq file are expressed in mdyne/Ĺ. For molecular dynamics simulations using software like AMBER, you may need to convert these values to kcal/(mol·Ĺ˛). Use the conversion factor 143.836 for this purpose: Force Constant (kcal/(mol.A˚˛))=Force Constant (mdyne/A˚)×143.836
5. Calculation of EHLQM1+ptch23 Using ORCAThe total QM/MM energy in electrostatic embedding is calculated as follows [3,4]: EQM/MM = EHLQM1+ptch23 + ECLMM123,q1=0 − EHLMM1,q1=0 where: · EHLQM1+ptch23 is the QM energy of system 1 (the QM system), truncated by hydrogen link (HL) atoms, and embedded in a set of point charges representing systems 2 and 3 (the MM systems). This term excludes the self-energy of the point charges. · EHLMM1,q1=0 is the MM energy of the QM system, also truncated by HL atoms, but with no electrostatic interactions. · ECLMM123,q1=0 is the classical energy of all atoms in the system, using carbon link (CL) atoms, with the charges of the QM system set to zero (to avoid double counting electrostatic interactions). · To calculate EHLQM1+ptch23 using ORCA, the interactions of point charges with the QM system must be included. ORCA reads these point charges from a file that specifies their coordinates and magnitudes. To enable this, include the following keyword in your ORCA input file: %pointcharges "pointcharges.pc"
Below is an example ORCA input file for optimizing methane in the presence of a water molecule (represented as point charges) at the TPSS/def2-SVP level with an auxiliary RIJ basis set:
! TPSS OPT def2-SVP def2/J NormalPrint NormalSCF
%scf MaxIter 300 CNVDIIS 1 CNVSOSCF 1 end
%output print[p_mos] true print[p_basis] 5 end
%pal nprocs 4 end
%pointcharges "pointcharges.pc"
* xyz 0 1 C -3.85992 0.91702 -0.00631 H -3.00431 0.24234 -0.17317 H -3.68963 1.86274 -0.54597 H -3.97234 1.12877 1.07018 H -4.78269 0.44545 -0.38236 *
The pointcharges.pc file specifies the number of point charges, their magnitudes (in atomic units), and their positions (in Angstroms). Note that interactions between point charges are not included in the nuclear energy calculation, as these are typically handled by the MM program. Sample pointcharges.pc File 3 -0.834 -1.11423 -1.35017 -0.22015 0.417 -0.92917 -0.82211 0.57773 0.417 -1.85814 -1.90905 0.06976
6. References[1] F. Neese, The ORCA program system, WIREs Comput. Mol. Sci. 2 (2012) 73–78. https://doi.org/10.1002/wcms.81. [2] T. Lu, F. Chen, Multiwfn: A multifunctional wavefunction analyzer, J. Comput. Chem. 33 (2012) 580–592. https://doi.org/10.1002/jcc.22885. [3] U. Ryde, The coordination of the catalytic zinc in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations., J. Comput. Aided. Mol. Des. 10 (1996) 153–164. https://doi.org/10.1007/BF00402823. [4] U. Ryde, M.H.M. Olsson, Structure, strain, and reorganization energy of blue copper models in the protein, Int. J. Quantum Chem. 81 (2001) 335–347. https://doi.org/10.1002/1097-461X(2001)81:5<335::AID-QUA1003>3.0.CO;2-Q.
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Department of Chemistry, Faculty of Science, University of Kurdistan |
Mehdi Irani Teaching duties Methods |