# FAQ¶

## What’s the difference between MOPAC in AMS2019 and in previous versions (AMS2018)?¶

In AMS2019 we have made a new MOPAC library, which is fully integrated as an Engine with the AMS driver and our GUI. This new MOPAC works much faster as a pre-optimizer and with any AMS driver functionality. This version of MOPAC is based on the original MOPAC code of Dr. Stewart and contains much but not all of the functionality. In AMS2019, MOPAC is included with the DFTB module. With AMS2018 it is possible to use the openmopac binaries, with all original functionality, and MOPAC could also be used as an external engine. The MOPAC binaries in AMS2018 were free of charge for academic groups with any other license. In AMS2018 there is no support for the new integrated MOPAC Engine.

Older ADF Modeling License suite licenses could also contain the external MOPAC binary and corresponding GUI support.

## How to use keywords from the MOPAC manual?¶

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 http://openmopac.net/manual/allkeys.html):

### Keywords used in MOPAC2012¶

& | Turn next line into keywords |

+ | Add another line of keywords |

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 |

C.I.=nC.I.=( n,m) |
A multi-electron configuration interaction specified |

CHAINS(text) |
In a protein, explicitly 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 |

DRC DRC= n.nnn |
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,m.mm,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 |

H-PRIORITY H-PRIORITY= n.nn |
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 |

IRC IRC= n |
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=(n_{1},n_{2},n_{3}) |
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(n_{1},n_{2}) |
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/m^{2 }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 |

THERMO THERMO( nnn)THERMO( nnn,mmm) THERMO( nnn,mmm,lll) |
Perform a thermodynamics calculation |

THREADS=n |
Set the number of threads to be used in parallelization to n |

TIMES | Print times of various stages |

T-PRIORITY T-PRIORITY= n.nn |
Time takes priority in DRC |

TRANS TRANS= n |
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 |

## Which properties from MOPAC can be visualized with the GUI?¶

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.