Orca

Orca is a free software for all types of QM calculations.
Documentation and tutorials are here: https://www.orcasoftware.de/tutorials_orca

The current version is 5.0.3.
It is installed on Aurora:
module add GCC/11.2.0 OpenMPI/4.1.1 ORCA/5.0.3-static
Then, it is run by
orca input_file >output

Avogadro is a good option to illustrate Orca output

This is a simple sample input file:

! RHF def2-SVP          # Level of theory.
! SP                             # Single-point energy calculation; it is default or
! OPT                          # Geometry optimisation

* xyz 0 1                     # Charge, and multiplicity followed by coordinates in Å (can be changed to a.u. by %coords Units bohrs)
h           1.57623125918282     -1.40098816005358      1.92944524289998
c           3.11804788185000     -1.26044723466300      3.33347664459600
h           4.63927730299500     -2.45475405971100      2.62293967273200
h           3.85126156558200      0.66329382213900      3.40150678020000
h           2.59270405690800     -1.91429242685700      5.21564372964000
*

Alternatively, internal coordinates can be used:
* int 0 2
O 0 0 0 0.0       0.0 0.0
H 1 0 0 0.9903 0.0 0.0
*

Alternatively, an xyz file can be used:
* xyzfile 0 2 hydroxide.xyz

File:
2 # number of atoms; next line blank or title

0
O 0 0 0
H 0 0 0.9903

Alternatively, an pdb file can be used:
* pdbfile 0 2 hydroxide.pdb

Input file is not case sensitive.

Constraints:
%geom
Constraints
   {B 0 1 1.25 C}    # Bond length constraint
   end
end

Cartesian coordinate constraints:
%geom
Constraints
{ C 3 C }    # Atom 4 is fixed
    {C 10:17 C}   # A list of atoms is also allowed
    end
end

Note that Orca number atoms starting with 0, which may be very confusing in the beginning.

Options

Use RI and RIJCOSX (exchange)
!B3LYP def2-SVP def2/J RIJDX RIJCOSX
In fact, this is default for DFT; to turn it off, use !NORI and !NOCOSX

Dispersion correction
!D3 or !D4

Increase amount printed out (e.g. to print orbitals)
!HF def2-SVP Largeprint

Frequency calculation
!FREQ
!TightOpt or !VeryTightOpt may remove imaginary freqs

Implicit solvent (COSMO is no longer any option)
!CPCM(solvent)
or
%CPCM
EPSILON 80
REFRAC 1.33
END
or
%CPCM SMD TRUE
SMDSolven "solvent"
END

Relativistic corrections
!B3LYP ZORA ZORA-def2-TVP RIJDX SARC/J

DLPNO CC
!DLPNO-CCSD(T) def2-TZVPP def2-TZVPP/C

Change maximum number of geometry steps
%geom
maxiter 1
end

Cartesian optimisation
! COpt

SCF options
%scf
MaxIter 300
CNVDIIS 1
CNVSOSCF 1
end

%scf
        guess moread
        moinp "TS2-opt.gbw"
        maxiter 999
end

Level shift
%scf
CNVShift true # default = true
LShift 0.1 # default = 0.25
ShiftErr 0.1 #default = 0.0
# more convenient:
Shift Shift 0.1 ErrOff 0.1 end
end

Output options
%output
print[p_mos] true
print[p_basis] 5
end

Paralell calculations
%pal
nprocs 20               #Maximum number of cores of your machine.
end

or simply pal16, e.g.
!QMMM PBE0 6-31G* D3ZERO Opt pal16

Point charges with file reference
%pointcharges "pointcharges.pc"

File pointcharges.pc
418 # number of point charges
0.294300             6.494988     -4.096926     -5.179739 # charge and coordinates
0.164200             7.320798     -3.807798     -6.874823
0.164200             6.417509     -5.943188     -4.694079
...
No special ending
Atomic units

Geometry options
%geom
MaxIter 200
TS_search EF
# ! OptTs
TolE 5e-6
TolRMSG 1e-4
TolMaxG 3e-4
TolRMSD 2e-3
TolMaxD 4e-3
inhess GFNFF
end

TS optimisation
!QMMM PBE0 6-31G* D3ZERO OptTS SlowConv TightSCF pal16

Scan a reaction coordinate
%geom scan
B 11 2275 [2.0 1.9 1.8] end
end

Example for a system that is hard to converge the SCF (nitrogenase)
! TPSS D4 DEF2-SV(P) UKS! ENGRAD! NOTRAH! SlowConv! TightSCF%scf MaxIter 1000 DIISMaxEq 40 DirectResetFreq 1end%PAL NPROCS 48 END*pdbfile -2 1 qm_1_h.pdb

%MaxCore 2000

Output
File *.in contains the input
*.out the output (very long)
*.engrad energy, gradient and coordinates.

*** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
Dispersion correction           -0.077894975
FINAL SINGLE POINT ENERGY     -2474.907119623929
FINAL SINGLE POINT ENERGY (QM/MM)    -2507.427748516620

Scans:
*** OPTIMIZATION RUN DONE ***
RELAXED SURFACE SCAN STEP   6

RELAXED SURFACE SCAN RESULTS
----------------------------

Column   1: NONAME

The Calculated Surface using the 'Actual Energy'
   2.00000000 -2507.39966580
   1.90000000 -2507.42805085
   1.80000000 -2507.42978390

The Calculated Surface using the SCF energy
   2.00000000 -2474.80098184
   1.90000000 -2474.82795119
   1.80000000 -2474.82969327

QM/MM with Orca
Described in the Orca manual under

8.13 ORCA Multiscale Implementation

You need a prmtop file and a pdb file (and preferably a syst1 file)

1. Make an Orca input file:
!QMMM PBE0 6-31G* D3ZERO

%qmmm
    ORCAFFFilename   "prmtop3.ORCAFF.prms"
    QMAtoms          { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
    ActiveAtoms      { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
end

*pdbfile 0 1 pdb3.pdb

Made from the syst1 file, but renumbering to start on 0, changing "-" to ":" and removing link atoms.

2. Convert prmtop file to Orca format
orca_mm -convff -AMBER prmtop
Gives you the file prmtop3.ORCAFF.prms

3. Finally start Orca with
orca orca.in >orca.out

This does additive QM/MM and electrostatic embedding.
You may change the charges around the junction atoms (p. 375). Orca implements the Charge Shift (CS; default), Redistributed charge and dipole (RCD), as well as the Z0, Z1, Z2 and Z3 methods.
%qmmm
   chargeAlgeration RCD
end

4. Output (in *.out):
FINAL SINGLE POINT ENERGY (MM)      -32.522715848742
FINAL SINGLE POINT ENERGY     -2474.898029955347
FINAL SINGLE POINT ENERGY (QM/MM)    -2507.420745804089
*** OPTIMIZATION RUN DONE ***

Protein free
!QMMM PBE0 6-31G* D3ZERO OPT
%PAL NPROCS 24 END
%qmmm
    ORCAFFFilename   "prmtop3.ORCAFF.prms"
    QMAtoms          { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
    ActiveAtoms      { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
      ExtendActiveRegion        distance
      Dist_AtomsAroundOpt       6.
      PrintOptRegionExt         true
end
*pdbfile 0 1 pdb3.pdb

NEB calculations
!QMMM PBE0 6-31G* D3ZERO NEB-TS SlowConv TightSCF pal16
%neb
   Product_PDBFile "orca-prod.pdb"
   TS_PDBFile "TSGuess.pdb"
   NImages 8
   NEB_TS false
end
%qmmm
    ORCAFFFilename   "prmtop3.ORCAFF.prms"
    QMAtoms          { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
    ActiveAtoms      { 0:33
                       642:653
                       2238:2239
                       2248:2275
                       4716:4718 } end
end

*pdbfile 0 1 orca-reac.pdb

Output in orca.out
                    ***        THE NEB OPTIMIZATION HAS CONVERGED     ***
                         PATH SUMMARY
5     4.727   -2507.39972     20.33       0.02832   0.00417 <= CI
              INFORMATION ABOUT SADDLE POINT
Energy                                    .... -2507.39972016 Eh

Useful greps

# Greps for all occurrences of convergence parameters in ORCA as they are displayed after each geom opt step

grep -A8 "Geometry convergence"

grep " MAX gradient"

grep "ENERGY (QM/MM)" $1 | tail -n 1 ;

neb_energies() {

# Gets the energies of the last step of an ORCA .NEB.log file and creates a temporary path vs energy file.

# $1: file to grep for QM/MM energies

tail -n 30 $1 | grep energy | tail -n 1 | sed 's/energy : //g'| tr -s ' ' '\n' > energies ;

tail -n 30 $1 | grep distance $1 | tail -n 1 | sed "s/distance : //g" | tr -s ' ' '\n' > abscissa ;

paste abscissa energies > tmp_path_energies ;

rm -fr abscissa energies ;

}