In ADFInput in the Details → Run script tab, you can change the MOPAC input file before submitting the calculation.
A list of MOPAC keywords (from

Keywords used in MOPAC2012

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0SCF Read in data, then stop
1ELECTRON Print final one-electron matrix
1SCF Do one scf and then stop
ADD-H Add hydrogen atoms (intended for use with organic compounds)
A0 Input geometry is in atomic units
AIDER Read in ab-initio derivatives
AIGIN Geometry must be in gaussian format
AIGOUT In arc file, include ab-initio geometry
ALLBONDS Print final bond-order matrix, including bonds to hydrogen
ALLVEC Print all vectors (keywords vectors also needed)
ALT_A=A In PDB files with alternative atoms, select atoms A
ALT_R=A In PDB files with alternative residues, select residues A
ANGSTROMS Input geometry is in Angstroms
AUTOSYM Symmetry to be imposed automatically
AUX Output auxiliary information for use by other programs
AM1 Use the AM1 hamiltonian
BAR=n.nn reduce bar length by a maximum of n.nn%
BCC (Unique) Solid is body-centered cubic (used by BZ)
BFGS Optimize geometries using bfgs procedure
BIGCYCLES=n Do a maximum of n big steps
BIRADICAL System has two unpaired electrons
BONDS Print final bond-order matrix
BZ Generate a file for use by program BZ
CAMP Use Camp-King converger in SCF
CARTAB Print point-group character table
A multi-electron configuration interaction specified
CHAINS(text) In a protein, explicitely define the letters of chains.
CHECK Report possible faults in input geometry
CHARGE=n Charge on system = n (e.g. NH4 = +1)
CHARGES Print net charge on system, and all charges in the system
CHARST Print details of working in CHARST
CIS C.I. uses 1 electron excitations only
CISD C.I. uses 1 and electron excitations
CISDT C.I. uses 1, 2 and 3 electron excitations
COMPFG Print heat of formation calculated in COMPFG
COSCCH Add in COSMO charge corrections
COSWRT Write details of the solvent accessible surface to a file
CUTOFP=n.nn Madelung distance cutoff is n .nn Angstroms
CUTOFF=n.nn In MOZYME, the interatomic distance where the NDDO approximation stops
CYCLES=n Do a maximum of n steps
CVB In MOZYME. add and remove specific bonds to allow a Lewis or PDB structure.
DAMP=n.nn n MOZYME. damp SCF oscillations using a factor of n.nn
DATA=text Input data set is re-defined to text
DCART Print part of working in DCART
DDMAX=n.nn See EF code
DDMIN=n.nn Minimum trust radius in a EF/TS calculation
DEBUG Debug option turned on
DEBUG PULAY Print working in PULAY
DENOUT, DENOUTF Density matrix output
DENSITY Print final density matrix
DERI1 Print part of working in DERI1
DERI2 Print part of working in DERI2
DERITR Print part of working in DERIT
DERIV Print part of working in DERIV
DERNVO Print part of working in DERNVO
DFORCE Force calculation specified, also print force matrix.
DFP Use Davidson-Fletcher-Powell method to optimize geometries
DISEX=n.nn Distance for interactions in fine grid in COSMO
DISP Print the hydrogen bonding and dispersion contributions to the heat of formation
DMAX=n.nn Maximum stepsize in eigenvector following
DOUBLET Doublet state required
Dynamic reaction coordinate calculation
DUMP=nn.nn Write restart files every n seconds
ECHO Data are echoed back before calculation starts
EF Use ef routine for minimum search
EIGEN Print canonical eigenvectors instead of LMOs in MOZYME calculations
EIGS Print all eigenvalues in ITER
ENPART Partition energy into components
EPS=n.nn Dielectric constant in COSMO calculation
ESP Electrostatic potential calculation
ESPRST Restart of electrostatic potential
ESR Calculate RHF spin density
EXCITED Optimize first excited singlet state
EXTERNAL=name Read parameters off disk
FIELD=(n.nn,,l.ll) An external electric field is to be used
FILL=n In RHF open and closed shell, force M.O. n to be filled
FLEPO Print details of geometry optimization
FMAT Print details of working in FMAT
FOCK Print last Fock matrix
FREQCY Print symmetrized Hessian in a FORCE calculation
FORCE, FORCETS Calculate vibrational frequencies
GEO-OK Override some safety checks
GEO_REF=<text> Use native structure as reference
GNORM=n.nn Exit when gradient norm drops below n .n kcal/mol/Angstrom
GRADIENTS Print all gradients
GRAPH Generate unformatted file for graphics
GRAPHF Generate formatted file for graphics suitable for  Jmol and MOPETE.
HCORE Print all parameters used, the one-electron matrix, and two-electron integrals
HESSIAN Print Hessian from geometry optimization
HESS=n Options for calculating Hessian matrices in EF
Heat of formation takes priority in DRC
HTML Write a web-page for displaying and editing a protein
HYPERFINE Hyperfine coupling constants to be calculated
INT Make all coordinates internal coordinates
INVERT Reverse all optimization flags
IONIZE Do not use – use SITE=(IONIZE) instead
Intrinsic reaction coordinate calculation
ISOTOPE Force matrix written to disk (channel 9 )
ITER Print details of working in ITER
ITRY=nn Set limit of number of SCF iterations to n
IUPD=n Mode of Hessian update in eigenvector following
KINETIC=n.nnn Excess kinetic energy added to DRC calculation
KING Use Camp-King converger for SCF
LARGE Print expanded output
LBFGS Use the low-memory version of the BFGS optimizer
LET Override certain safety checks
LEWIS Print the Lewis structure
LINMIN Print details of line minimization
LOCALIZE Print localized orbitals.  These are also called Natural Bond Orbitals or NBO
LOCATE-TS Given reactants and products, locate the transition state connecting them
LOG Generate a log file
MECI Print details of MECI calculation
MERS=(n1,n2,n3) Keyword for BZ
METAL=(a[,b[,c[…]]]) Make specified atoms 100% ionic
MICROS=n Use specific microstates in the C.I.
MINMEP Minimize MEP minima in the plane defined
MMOK Use molecular mechanics correction to CONH bonds
MNDO Use the MNDO hamiltonian
MNDOD Use the MNDO-d hamiltonian
MODE=n In EF, follow Hessian mode no. n
MOL_QMMM Incorporate environmental effects in the QM/MM approach
MOLDAT Print details of working in MOLDAT
MOLSYM Print details of working in MOLSYM
MOPAC Use old MOPAC definition for 2nd and 3rd atoms
MOZYME Use the Localized Molecular Orbital method to speed up the SCF
MS=n In MECI, magnetic component of spin
MULLIK Print the Mulliken population analysis
N**2 In excited state COSMO calculations, set the value of N**2
NLLSQ Minimize gradients using NLLSQ
NOANCI Do not use analytical C.I. derivatives
NOGPU Do not use GPU acceleration
NOLOG Suppress log file trail, where possible
NOMM Do not use molecular mechanics correction to CONH bonds
NONET NONET state required
NONR Do not use Newton-Raphson method in EF
NOOPT, NOOPT-X Do not optimize the coordinates of all atoms of type X
NOREOR In symmetry work, use supplied orientation
NORESEQ Suppress the default re-sequencing of atoms to the PDB sequence
NOSWAP Do not allow atom swapping when GEO_REF is used
NOSYM Point-group symmetry set to C1
NOTHIEL Do not use Thiel’s FSTMIN technique
NOTXT Remove any text from atom symbols
NOXYZ Do not print Cartesian coordinates
NSPA=n Sets number of geometric segments in COSMO
NSURF Number of surfaces in an ESP calculation
OCTET Octet state required
OLDCAV In COSMO, use the old Solvent Accessible Surface calculation
OLDENS Read initial density matrix off disk
OLDFPC Use the old fundamental physical constants
OLDGEO Previous geometry to be used
OMIN=n.nn In TS, minimum allowed overlap of eigenvectors
OPEN(n1,n2) Open-shell UHF or RHF calculation requested
OPT, OPT-X Optimize the coordinates of all atoms of type X
P=n.nn An applied pressure of n.nn Newtons/m2 to be used
PDB Input geometry is in protein data bank format
PDB=(text) User defined chemical symbols in protein data base
PDBOUT Output geometry in pdb format
PECI C.I. involves paired excitations only
PI Resolve density matrix into σ, π, and δ components
pKa Print the pKa for ionizable hydrogen atoms attached to oxygen atoms
PL Monitor convergence of density matrix in ITER
PM3 Use the MNDO-PM3 Hamiltonian
PM6 Use the PM6 Hamiltonian
PM6-D3 Use the PM6 Hamiltonian with Grimme’s corrections for dispersion
PM6-DH+ Use the PM6 Hamiltonian with corrections for dispersion and hydrogen-bonding
PM6-DH2 Use the PM6 Hamiltonian with corrections for dispersion and hydrogen-bonding
PM6-DH2X Use PM6 with corrections for dispersion and hydrogen and halogen bonding
PM6-D3H4 Use PM6 with Řezáč and Hobza’s D3H4 correction
PM6-D3H4X Use PM6 with Brahmkshatriya, et al.’s D3H4X correction
PMEP Complete semiempirical MEP calculation
PM7 Use the PM7 Hamiltonian
PM7-TS Use the PM7-TS Hamiltonian (only for barrier heights)
PMEPR Complete semiempirical MEP in a plane to be defined
POINT=n Number of points in reaction path
POINT1=n Number of points in first direction in grid calculation
POINT2=n Number of points in second direction in grid calculation
POLAR Calculate first, second and third order polarizabilities
POTWRT In ESP, write out electrostatic potential to unit 21
POWSQ Print details of working in POWSQ
PRECISE Criteria to be increased by 100 times
PRESSURE Apply pressure or tension to a solid or polymer
PRNT=n Print details of geometry optimization in EF
PRTCHAR Print charges in ARC file
PRTINT Print interatomic distances
PRTMEP MEP contour data output to <filename>.mep
PRTXYZ Print Cartesian coordinates
PULAY Use Pulay’s converger to obtain a SCF
QMMM Incorporate environmental effects in the QM/MM approach
QPMEP Charges derived from Wang-Ford type AM1 MEP
QUARTET Quartet state required
QUINTET Quintet state required
RAPID In MOZYME geometry optimizations, only use atoms being optimized in the SCF
RECALC=n In EF, recalculate Hessian every n steps
RE-LOCAL, RE-LOCAL=n During and at end of MOZYME calculation, re-localize the LMOs
RELSCF Default SCF criterion multiplied by n
REORTHOG In MOZYME, re-orthogonalize LMO’s each 10 SCF calculations.
RESEQ Re-arrange the atoms to match the PDB convention
RESIDUES Label each atom in a polypeptide with the amino acid residue
RESTART Calculation restarted
RHF Use Restricted Hartree-Fock methods
RM1 Use the RM1 Hamiltonian
RMAX=n.nn In TS, maximum allowed ratio for energy change
RMIN=n.nn In TS, minimum allowed ratio for energy change
ROOT=n Root n to be optimized in a C.I. calculation
RSCAL In EF, scale p-RFO to trust radius
RSOLV=n.nn Effective radius of solvent in COSMO
SADDLE Optimize transition state
SCALE Scaling factor for van der waals distance in ESP
SCFCRT=n.nn Default SCF criterion replaced by the value supplied
SCINCR=n.nn Increment between layers in ESP
SEPTET Septet state required
SETPI In MOZYME, some π bonds are explicitly set by the user
SETUP Extra keywords to be read from setup file
SEXTET Sextet state required
SHIFT=n.nn a damping factor of n defined to start SCF
SHUT <file> Send a command to MOPAC to make a restart and density file, then stop.
SIGMA Minimize gradients using SIGMA
SINGLET Singlet state required
SITE=(text) Define ionization state of residues in proteins
SLOG=n.nn In BFGS optimization, use fixed step of length n .nn
SLOPE Multiplier used to scale MNDO charges
SMOOTH In a GRID calculation, remove artifacts caused by the order in which points are calculated
SNAP Increase precision of symmetry angles
SPARKLE Use sparkles instead of atoms with basis sets
SPIN Print final UHF spin matrix
START_RES(text) Define starting residue numbers in a protein, if different from the default
STATIC Calculate Polarizability using electric fields
STEP Step size in path
STEP1=n.nnn Step size n for first coordinate in grid calculation
STEP2=n.nnn Step size n for second coordinate in grid calculation
STO3G Deorthogonalize orbitals in STO-3G basis
SUPER Print superdelocalizabilities
SWAP This keyword is now obsolete, see NOSWAP
SYBYL Output a file for use by Tripos’s SYBYL program
SYMAVG Average symmetry equivalent ESP charges
SYMOIR Print characters of eigenvectors and print number of I.R.s
SYMTRZ Print details of working in subroutine SYMTRZ.
SYMMETRY Impose symmetry conditions
T=n[M,H,D] A time of n seconds requested
Perform a thermodynamics calculation
THREADS=n Set the number of threads to be used in parallelization to n
TIMES Print times of various stages
Time takes priority in DRC
The system is a transition state (used in thermodynamics calculation)
TRIPLET Triplet state required
TS Using EF routine for TS search
UHF Use the Unrestricted Hartree-Fock method
VDW(text) Van der waals radius for atoms in COSMO defined by user
VDWM(text) Van der waals radius for atoms in MOZYME defined by user
VECTORS Print final eigenvectors
VELOCITY Supply the initial velocity vector in a DRC calculation
WILLIAMS Use Williams surface
X-PRIORITY=n.nn Geometry changes take priority in DRC
XENO Allow non-standard residues in proteins to be labeled.
XYZ Do all geometric operations in Cartesian coordinates
Z=n Number of mers in a cluster

Besides facilitating building molecules, our GUI can also visualize the progress of geometry optimizations, MOPAC charges, and IR modes. Geometry optimization can also be done interactively, e.g. to pre-optimize your molecule or periodic system.