ORCA

ORCA is a flexible, efficient, and easy-to-use general-purpose tool for quantum chemistry, emphasizing the spectroscopic properties of open-shell molecules [1]. It contains many standard quantum chemical methods, e.g., semiempirical, DFT, and single- and multi-reference correlated ab initio methods. It can also treat environmental and relativistic effects.

Homepages:

https://orcaforum.kofo.mpg.de/app.php/portal

https://www.faccts.de/

ORCA tutorials - Compatible with ORCA 5.0!:

https://www.orcasoftware.de/tutorials_orca/index.html

1. Installation of ORCA 5.03 on UBUNTU, by Javad Shirazi

1.1 Switch to the root user, change your working directory to /opt/, make a directory in the /opt/ directory, and name it orca.

sudo su

cd /opt/

mkdir orca

cd orca/

1.2 Copy the installation files into the orca directory. You can download them from https://orcaforum.kofo.mpg.de/app.php/portal or copy them from a local machine if you have already downloaded them. For example, we use the following command to copy the installation files from a local machine.

scp darvin@172.16.13.150:/home/darwin/programs/Orca-Linux/* .

1.3 Extract the installation files.

tar xvf orca_5_0_3_linux_x86-64_openmpi411_part1.tar.xz

tar xvf orca_5_0_3_linux_x86-64_openmpi411_part2.tar.xz

tar xvf orca_5_0_3_linux_x86-64_openmpi411_part3.tar.xz

mv orca_5_0_3_linux_x86-64_openmpi411_part1/* .

mv orca_5_0_3_linux_x86-64_openmpi411_part2/* .

mv orca_5_0_3_linux_x86-64_openmpi411_part3/* .

\rm -r orca_5_0_3_linux_x86-64_openmpi411_part*

1.4 Add a group and name it 'orca'.

groupadd -g 2222 orca

1.5 Add your user ID to the orca group. In the following command, 'mehdi' is my user-id.

usermod -a -G orca mehdi

1.6 Change the permission and owner of the orca directory. In the following, 2222 is the orca group id that we created in step ‎1.4.

cd ../

chown -R root:2222 orca

chmod -R 750 orca

1.7 Install the gcc compiler.

apt install gcc

apt-get install gcc build-essential

1.8 Parallelization of ORCA

1.8.1 Download and install openmpi.

cd /opt/

wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz

tar xvf openmpi-4.1.1.tar.gz

cd openmpi-4.1.1/

./configure --prefix=/opt/.openmpi

make all install

cd ../

chown -R root:2222 openmpi-4.1.1

chmod -R 750 openmpi-4.1.1

1.8.2 Switch to your user and insert the path of ORCA and openmpi into your .bashrc file.

su mehdi

echo '#ORCA5.02' >> ~/.bashrc

echo 'export PATH=/opt/orca/:$PATH; export LD_LIBRARY_PATH=/opt/orca/:$LD_LIBRARY_PATH' >> ~/.bashrc

echo 'export PATH=/opt/.openmpi/bin:$PATH; export LD_LIBRARY_PATH=/opt/.openmpi/lib:$LD_LIBRARY_PATH' >> ~/.bashrc

echo 'alias orca=" /opt/orca//orca " ' >> ~/.bashrc

source ~/.bashrc

2. Calculations of RESP charges using ORCA and Multiwfn

To calculate RESP charges with ORCA [1] and Multiwfn [2], you can execute the following command in a directory with ORCA calculations. This generates a .moledn file (job.molden.input) from the wave function file of the ORCA calculations (job.gbw in our case).

orca_2mkl job -molden

mv job.molden.input job.molden

Then extract the RESP charge from the .moleden file using the Multiwfn program. The charges are located in the last column of the job.chg file.

Multiwfn3.7 <<EOF

job.molden

EOF

You may need to change the above script if the radii of some atoms are missed. Then, you need to manually enter the atoms' radii or scale them as the program suggests.

You may also encounter some library errors in UBUNTU before running Multiwfn. If so, execute the following commands.

sudo su

apt-get update -y

apt-get install -y libmotif-common

apt-get install -y libxm4

apt-get install libgfortran3

3. Calculation of E^HL_QM1+ptch23 by ORCA

The total QM/MM energy in electrostatic embedding is calculated as [3,4]

E_QM/MM = E^HL_QM1+ptch23 + E^CL_MM123,_q₁₌₀ − E^HL_MM1,_q₁₌₀ (1)

where E^HL_QM1+ptch23 is the QM energy of system 1 (the QM system), truncated by hydrogen link (HL) atoms and embedded in the set of point charges representing systems 2 and 3 (the MM systems) but excluding the self-energy of the point charges. E^HL_MM1,_q₁₌₀ is the MM energy of the QM system, still truncated by HL atoms but without any electrostatic interactions. Finally, E^CL_MM123,_q₁₌₀ is the classical energy of all atoms in the system with carbon link (CL) atoms and with the charges of the QM system set to zero (to avoid double counting of the electrostatic interactions). To calculate the first term in the QM/MM energy (E^HL_QM1+ptch23) using ORCA do as follows.

In this case, we need to add the interactions of point charges with the QM system. The program reads the point charges from a file containing the coordinates and values of the point charges. To this, you need to add the % pointcharges "pointcharges.pc" keyword to your ORCA input file. Here are a sample input and point-charges file.

A sample ORCA input file for optimization of methane in the presence of water molecule as the point charge at the TPSS/def2SV(P) 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 following is the pointcharges.pc file. The first line gives the number of point charges. Each consecutive line gives the magnitude of the point charge (atomic units) and its position (Angstrom units!). When using an external point charge file, the interaction between the point charges is not included in nuclear energy. This behavior originates from QM/MM, where the MM program does the interactions among the point charges.

-0.834 -1.11423 -1.35017 -0.22015

0.417 -0.92917 -0.82211 0.57773

0.417 -1.85814 -1.90905 0.06976

4. 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.