Geometry Optimization and Transition-State Keywords in the Jaguar Input File

  • Overview
  • Examples

Many of the keyword settings for optimization of minimum-energy structures and transition states described in this subsection can be made from the GUI, as described in Jaguar Optimizations and Scans, which also contains more details about the methods used for optimizations.

Table 1 contains general optimization keywords that apply to all kinds of optimizations. Most default values for the integer keywords are indicated in bold italics, and only the values listed in the table are allowed. In cases where the default is different for optimizations to minimum-energy structures than it is for transition-state optimizations, both defaults are in bold italics, and the cases for which each is a default are explained in the keyword description.

Table 1. General geometry optimization keywords

Keyword

Value

Description

igeopt

0

Do not optimize molecular geometry

 

1

Optimize minimum-energy structure

 

−1

Calculate forces but do not perform geometry optimization

 

2

Optimize transition-state geometry

nogas

0

For optimizations in solution, perform gas phase geometry optimization first (to get accurate solvation energy). If nogas is set to 0 for single point energy (igeopt=0) or force calculations (igeopt=-1) in solution, nogas=2 is used instead.

 

1

For optimizations in solution, skip gas phase geometry optimization and compute solvation energies using esolv0 value (from input file) as gas phase energy (should yield same structure as nogas=0). This option can also be used with single point energy (igeopt=0) or force calculations (igeopt=-1) in solution.

 

2

For optimizations in solution, skip gas phase geometry optimization and compute solvation energies using energy of initial structure as gas phase energy (should yield same structure as nogas=0). This is the default for the PCM solvation model, as well as single point energy (igeopt=0) or force calculations (igeopt=-1) in solution.

maxitg

>0

Maximum number of optimization iterations (maximum number of structures generated); default is 100.

nmder

0

If calculating forces, compute analytic derivatives of energy

 

1

If calculating forces, compute numerical derivatives of energy (obtained from calculations on 6 Natom perturbed geometries by moving each atom pertnd bohr in positive or negative x, y, or z direction)

 

2

Calculate frequencies numerically

intopt

0

Use Cartesian coordinates for optimization

 

1

Use internally generated redundant internal coordinates for optimization (including any from coord or connect sections, if they exist)

 

2

Use internal coordinates from input Z‑matrix for optimization (note: if geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom, intopt is reset to 1)

intopt_switch

0

Do not switch from internal coordinates to Cartesian coordinates during optimization.

 

1

Switch from internal coordinates to Cartesian coordinates during optimization if the optimization gets stuck.

 

2

Switch from internal coordinates to Cartesian coordinates during optimization if the calculation is converged to within a factor of intopt_switchfac of the convergence thresholds.

intopt_switchfac

10.0

Factor to be applied to convergence threshold to determine when to switch from internal coordinates to Cartesian coordinates during optimization. This applies for intopt_switch=2.

optcoord_newhist

0

Do not discard optimization history when switching coordinates.

 

1

Discard optimization history when switching coordinates.

 

2

Discard optimization history when switching coordinates and reset the Hessian if the calculation is an IRC calculation.

optcoord_update

0

Do not run checks for changing the internal coordinate set used for optimization.

 

1

Run checks for changing the internal coordinate set used for optimization.

nooptr

0

Optimize all bond lengths not specifically constrained in zmat section

 

1

Constrain (freeze) all bond lengths for optimization

noopta

0

Optimize all bond angles not specifically constrained in zmat section

 

1

Constrain (freeze) all bond angles for optimization

nooptt

0

Optimize all torsional angles not specifically constrained in zmat section

 

1

Constrain (freeze) all torsional angles for optimization

ip472

1

Do not save intermediate structures in the .mae output file.
 

2

Save intermediate structures in the .mae output file. This allows you to plot the energy during the course of the geometry optimization, using the Workflow Action Menu in Maestro.

props_each_step

0

Do not calculate properties at each step in a geometry optimization.

 

1

Calculate specified properties at each step in a geometry optimization. The properties you can calculate are ESP, Mulliken, and stockholder charges, multipole moments, and Fukui indices. The relevant keywords for the properties must also be included in the gen section (icfit, mulken, stockholder_q, ldips, fukui).

needgwd

0

Do not compute DFT grid weight derivatives

 

1

Compute DFT grid weight derivatives (and second derivatives for CPHF)

 

2

Compute DFT grid weight derivatives and gradient from grid translation (symmetry will be turned off)

 

3

Compute DFT grid weight derivatives and gradient from grid translation and rotation (symmetry will be turned off)

iaccg

2

Use convergence criteria shown in Table 7 This setting is used by default for gas-phase calculations, as well as SMD and PCM implicit solvent model calculations.

 

3

Use a looser criteria; a factor of 5 times the criteria in Table 7

 

4

A factor of 3 times the criteria in Table 7. This setting is

used by default for PBF implicit solvent model calculations.

 

5

Use tight criteria; a factor of 0.1 times the criteria in Table 7

scale_geoconv

1.0

Scaling factor for gradient convergence criteria. Each of the values in Table 7 is scaled by this factor.

geoconv_mode

standard

Use standard criteria for convergence, in which all five criteria must be met (energy difference, maximum gradient, rms gradient, maximum displacement, rms displacement).

 

flexible

Assess convegence based on a score, with one point for meeting a criterion, an extra point if a gradient or displacement criterion is met to 0.2 of the threshold, an extra point if the energy change is less than 0.05 of threshold and another if it is less than 0.005 of threshold. The optimization is converged if the score is 5 or more points.

ignore_displacement_criteria

0

Convergence criteria set for displacement RMS (gconv6) and maximum displacement (gconv5) are used when considering convergence.

 

1

Convergence criteria for displacement RMS (gconv6) and maximum displacement (gconv5) are not used when considering convergence.

nops_opt_switch

>0

Specifies convergence cutoff for switching from pseudospectral to analytic integral evaluation in a geometry optimization. The value multiplies the standard convergence criterion, and a switch to nops=1 is made when convergence is reached with the scaled convergence cutoff. The value must be greater than 1 for switching to take place. Not available with IRC or check_min > 0.

ngeorestart

≥0

Maximum number of automatic restarts used for a “stuck” geometry optimization. Restarting discards the Hessian history and sets iacc=1. Default is 1

nogdiis

0

Use GDIIS method (Geometry optimization by Direct Inversion in the Iterative Subspace) [203] to get new geometry

 

1

Don’t use GDIIS method

ilagr

<0

Zero out gradients along frozen coordinates

 

0 or 1

Project out gradient components in constrained coordinates

 

>1

Apply constraints using Lagrange multipliers

constraint_exponent

2

Exponent of monomial in flat-bottomed constraints. The default value produces a harmonic constraint. See Applying Harmonic Constraints in Jaguar Calculations.

die_on_opt_failure

0

Allow the calculation to continue if the optimization does not converge. This permits analysis and subsequent use of the results. Default if nofail=1.

 

1

Stop the calculation if the optimization does not converge.

nofail_lowest_e

0

Return the geometry from the final iteration on geometry convergence failure, when nofail=1. Default if check_min>0.

 

1

Return the geometry that gives the lowest energy on geometry convergence failure, when nofail=1.

Table 2 lists keywords for analyzing geometry convergence and checking whether a minimum has been obtained when requested. The checking feature is not supported with dynamic constraints, or for scans or IRC calculations.

Table 2. Geometry optimization keywords for analyzing and checking convergence

Keyword

Value

Description

check_min

0

Do not check if the stationary point is a minimum.

 

1

Check for a minimum-energy structure by perturbing the initial converged geometry using the QM Hessian, which is calculated. The geometry is perturbed and re-optimized only if the QM Hessian contains negative eigenvalues, i.e., a lower energy geometry is found.

 

2

Check for a minimum-energy structure by perturbing all rotatable proper and improper torsions (excluding those in rings and double bonds). If the geometry can be perturbed in this way, a re-optimization is performed from this perturbed geometry.

 

3

Check for a minimum-energy structure by perturbing overlapping torsions and planar inversions (excluding those in rings and double bonds), and torsions involving potential internal hydrogen bonds in which the hydrogen atom (donor) is symmetrically placed between two acceptors. If the geometry can be perturbed in this way, a re-optimization is performed from this perturbed geometry.

check_min_update

0

The initial converged geometry is written to the output .mae. During optimization of the perturbed geometry, the output .mae file’s geometry will not be updated at each optimization step. The output .mae file will only be updated after the convergence of the perturbed structure.

 

1

The initial converged geometry is written to the output .mae. During optimization of the perturbed geometry, the output .mae file’s geometry will be updated at each optimization step. The output .mae file will also be updated after the convergence of the perturbed structure.

check_min_return

0

Do not check that the optimization of the perturbed structure returned to the initial converged structure.

 

1

Check that the optimization of the perturbed structure returned to the initial converged structure. If optimization of a perturbed geometry does return to the initial minimum, report this then exit from the optimization of the perturbed geometry. The criteria for checking are given by the keywords check_min_ergtol and check_min_geotol.

check_min_eigcut

-5.0

Cutoff value for negative Hessian eigenvalues, in cm−1. The Hessian used for this check is not mass-weighted, i.e., all masses are set to unity. The Hessian is represented in coordinates set by the intopt keyword. Eigenvalues above this cutoff do not count towards the number of negative eigenvalues used to perturb the geometry when check_min=1.

check_min_ergtol

0.00008

Energy tolerance in hartrees for determining if the geometry is returning back to the initial converged structure. If the energy difference between the perturbed geometry at any optimization step and the initial minimum is less than this amount, the geometry is considered to have returned to the initial structure.

check_min_geotol

0.02

Geometry tolerance in bohrs/radians for determining if the geometry is returning back to the initial converged structure. If the rms displacement between the perturbed geometry at any optimization step and the initial minimum is less than this amount, the geometry is considered to have returned to the initial structure.

check_min_pert

0.6

Magnitude of perturbation along the Hessian eigenvalue for check_min=1, in atom ic units.

check_min_target

0

Add perturbation values to the current angles for check_min=2 or 3. Default for check_min=2.

 

1

Use the perturbation value as a target angle for check_min=2 or 3. Default for check_min=3.

check_min_p_pert

20.0

Perturbation in degrees for torsional perturbations. Interpreted as a target value or an increment, depending on check_min_target.

check_min_p_tol

8.0

Tolerance in degrees for checking whether to perturb a torsion for check_min=3. If the value of the torsion deviates from planarity by less than this amount, the torsion is perturbed, or for H-bond perturbations, if the two torsions differ by more than this amount.

check_min_amide

0

Do not perturb amide bonds when check_min=3.

 

1

Perturb amide bonds when check_min=3.

check_min_hb_tar

0

Add perturbation values to H-bond dihedrals for check_min=3.

 

1

Use the perturbation value as a target H-bond dihedral for check_min=3.

check_min_hb_lim

90.0

Upper limit for potential H-bond dihedral angles. If the H-bond dihedral angles are greater in absolute value than this amount, they are not considered potential H-bonds and are not perturbed.

optverdict

0

Do not run analysis of geometry convergence.

 

1

Run analysis of geometry convergence and print report:

0: Monotonic convergence. Convergence OK.

1: Non-monotonic convergence. No erratic convergence was detected and the structure converged to an optimal structure. Convergence OK.

2: Erratic convergence but the optimization converged to an optimal structure. Convergence OK.

 

 

3: Convergence to a non-optimal structure. The difference between the converged energy and the minimum energy is less than 0.1 kcal/mol. Convergence OK for solvation, OK for pseudospectral if the difference is less than 0.01 kcal/mol, but not otherwise.

4: Converged to a non-optimal structure, whose energy is above the minimum energy by more than 0.1 kcal/mol. Convergence not OK.

No convergence category is written if the optimization ran out of iterations.

 

2

Print report on convergence at each iteration.

Table 3 lists keywords specific to transition-state optimizations. The keywords for checking the transition state (starting with ts_vet) require that the products and reactants are specified with zmat2 and zmat3 sections. These keywords check the transition state at convergence, and the calculation can be terminated if the checks do not pass (for example, before proceeding with an IRC calculation). Table 4 lists keywords that are used to specify the initial Hessian, control Hessian updating, and modify the Hessian when using it to update the geometry.

Table 3. Keywords for transition-state optimizations

Keyword

Value

Description

iqst

0

Perform standard (non-QST) transition-state search

 

1

Use quadratic synchronous transit (QST) methods to guide transition-state search. Sets itrvec to −5

qstinit

0.5

Distance of LST transition-state initial guess between reactant and product geometries. Range is 0.0 to 1.0.

ifollow

0

For each optimization iteration, select a new eigenvector to follow

 

1

For each optimization iteration, follow eigenvector that most closely correlates with one followed previously

itrvec

0

Select lowest Hessian eigenvector as transition vector

 

>0

Select eigenvector number itrvec as the transition vector (see Transition-State Optimizations). Sets ifollow to 1.

 

−1

Select lowest non-torsional eigenvector as the transition vector

 

−2

Select the lowest stretching eigenvector as the transition vector

 

−5

Select the eigenvector that best represents the reaction path (the QST vector)

 

−6

Select the eigenvector that best overlaps the active coordinates specified in the coord section (see Active Coordinates in the Jaguar Input File)

ts_vet

0

Do not do any transition state sanity checks

 

1

Check overlap of the transition vector with the QST vector, and stop if the check fails.

 

−1

Check overlap of the transition vector with the QST vector, and display results of the check only.
  2 Check interatomic distances for breaking or forming bonds. The bonds that are broken or formed are determined from the connectivity of the reactant and product structures. The bonds should be in a range appropriate to a transition state, determined by two distance factors, ts_vet_dist_fac0 and ts_vet_dist_fac1. If the ratio of the interatomic distance to the sum of their van der Waals radii is not between these two factors, the test fails.

 

−2

Check interatomic distances for bonds breaking or forming, and display results of the check only.
  3 Check both overlap and interatomic distances, and stop if the check fails.

 

−3

Check both overlap and interatomic distances, and display results of the check only.

ts_vet_dist_fac0

1.15

Factor for checking bonded distance. If the distance between two atoms is less than this factor times the sum of their van der Waals radii, they are considered to be at a bonded distance, rather than an appropriate distance for a transition state, and the test fails.

ts_vet_dist_fac1

1.8

Factor for checking nonbonded distance. If the distance between two atoms is more than this factor times the sum of their van der Waals radii, they are considered to be not bonded, rather than at an appropriate distance for a transition state, and the test fails.

ts_vet_olap_cut

0.33

Cutoff for overlap of the transition vector with the QST vector or with the active coordinates. If the overlap is less than this value, the test fails.
no_mul_imag_freq 0 Do not attempt to remove or prevent multiple imaginary frequencies for transition state structures.
  1 Attempt to remove multiple imaginary frequencies in a transition state search. This is done by nudging the structure in the direction of the eigenvectors for the imaginary frequencies.
no_mul_nudge_fac 1.0 Factor used to determine the magnitude of the displacement used to nudge the structure away from the geometry with multiple imaginary frequencies.
no_mul_hess_redo 0 Do not recalculate an analytic Hessian when nudging the structure.
  1

Recalculate an analytic Hessian after nudging the structure.
  2

Recalculate an analytic Hessian before nudging the structure.

 

Table 4. Keywords for control of the Hessian

Keyword

Value

Description

inhess

−1

Use Fischer-Almlöf guess for Hessian

 

0

Use Schlegel guess for Hessian (default only if no hess section exists)

 

1

Use unit matrix for initial Hessian

 

2

Use Cartesian input Hessian found in hess section (inhess=2 automatically if non-empty hess section exists)

 

4

Compute and use quantum mechanical Hessian
  6 Compute and use GFN2-xTB Hessian

input_hessian

fischer

Use Fischer-Almlöf guess for Hessian. Equivalent to setting inhess=−1.

 

schlegel

Use Schlegel guess for Hessian (default only if no hess section exists). Equivalent to setting inhess=0.

 

unit_matrix

Use unit matrix for initial Hessian. Equivalent to setting inhess=1.

 

input_cartesian

Use Cartesian input Hessian found in hess section (input_hessian=input_cartesian automatically if non-empty hess section exists). Equivalent to setting inhess=2.

 

true_hessian

Compute and use quantum mechanical Hessian. Equivalent to setting inhess=4.
  xtb Compute and use GFN2-xTB Hessian. Equivalent to setting inhess=6.

nhesref

>0

Number of lowest-frequency Hessian eigenvectors used in Hessian refinement (default is 0)

 

−1

Use the active coordinates specified in the coord section to refine the Hessian (see Active Coordinates in the Jaguar Input File).

pertnd

0.05

Displacement (in atomic units) used for Hessian refinement or calculations of numerical forces or frequencies.

irefhup

2

Refine initial Hessian using Powell updates [205]

 

3

Refine initial Hessian using mixed Murtagh-Sargent/Powell updates [206]

 

4

Refine initial Hessian using Murtagh-Sargent updates [207]

ihuptyp

0

Don’t update Hessian

 

1

Update Hessian each iteration using BFGS (Broyden-Fletcher-Goldfarb-Shanno) method [208] (default for minimum-energy structure optimizations)

 

2

Update Hessian using Powell method [205]

 

3

Update Hessian using mixed Murtagh-Sargent/Powell method [206] (default for transition-state optimizations and IRC calculations)

 

4

Update Hessian using Murtagh-Sargent method [207] (not recommended)

 

−1

Compute quantum mechanical Hessian at each geometry; sets inhess=4

irfo

0

Before using Hessian to update geometry, modify it by sign-flipping or reverting to an older Hessian [204]

 

1

Before using Hessian to update geometry, modify it by RFO (rational function optimization) level shifting [209]. Default for geometry optimizations that do not use dynamic constraints.

 

2

Before using Hessian to update geometry, modify it by P-RFO (partitioned rational function optimization) level shifting [209]. Default for transition-state searches. Automatically set for geometry optimizations that use dynamic constraints.

In order to avoid changing the geometry too much because of an unusually shaped potential well or an inaccuracy in the Hessian, Jaguar restricts the norm of the changes to the Cartesian or internal coordinates to be less than a certain trust radius, which is defined in atomic units (bohrs, radians). The trust radius can vary from one iteration to another (itradj=1) or it can be fixed (itradj=0). Keywords controlling the use of a trust radius are listed in Table 5.

Table 5. Keywords for trust radius adjustment

Keyword

Value

Description

itradj

0

Use same trust radius throughout optimization (default for minimum-energy structure optimizations)

 

1

Adjust trust radius using Culot/Fletcher heuristic [[208], [210]] (default for transition-state optimizations)

 

−1

Adjust trust radius using Simons’ cubic potential model [211] (not recommended with Jaguar)

itrcut

0

Apply trust radius by truncating Newton-Raphson step(s)

 

1

Apply trust radius by level shifting of Hessian to reduce resultant step size

trust

0.3

Initial trust radius, in atomic units (bohr and/or radians): if norm of proposed displacements exceeds trust radius, step size is reduced as described by itrcut (default is 0.3, except for transition-state optimizations, when it is 0.1)

tradmx

0.3

Maximum trust radius allowed during optimization for itradj>0; see trust information (default is 0.3, except for solvated cases, when it is 0.1)

tradmn

0.01

Minimum trust radius allowed during optimization for itradj>0; see trust information

tremx

0.25

Trust radius reduction criterion; if relative error between actual and predicted energy changes is more than tremx and itradj>0, trust radius is reduced

trgmx

0.0

Trust radius reduction criterion; for itradj>0 and trgmx>0, if absolute error in a component of predicted gradient exceeds trgmx hartrees/bohr, trust radius is reduced

treok

0.2

Criterion for increasing trust radius; if itradj=1 and relative error between actual and predicted energy changes is less than treok, trust radius is increased (treok default is 0.2)

trescal

2.0

Scale factor for trust radius adjustment; used only when itradj=1

If the trust radius is fixed, it remains the same throughout the optimization except when Jaguar determines that changing it will lead to better convergence for problem jobs. This setting is the default for optimizations to minimum-energy structures. If the trust radius is allowed to vary (the default for transition-state optimizations), Jaguar keeps geometry changes within the region that is well-described by the Hessian by increasing the trust radius when the Hessian is correctly predicting energy changes and decreasing it when the predictions are inaccurate.

Prevention of chemical reactions during a geometry optimization can be done with the stop_rxn keyword. This keywords turns on checking of the connectivity after each geometry step. If bonds have been broken or formed, the optimization is restarted with additional repulsive or harmonic restraint potentials to prevent the bonding change, based on the value of stop_rxn. The repulsive potential for keeping atoms apart has the form

while the potential for keeping atoms together is a flat-bottomed harmonic potential,

where r is the distance between the two atoms whose bonding change is to be prevented, r0 is the initial distance, and a is the half-width of the flat bottom. The parameters can be set by keywords, which are described in Table 6. The energies from these added terms are not included in the reported total energies, but are used, along with the forces from these terms, for optimization purposes. As the added energies are artificial and are often added to a region of the potential surface that is quite steep, the results can be sensitive to the parameters used and to other circumstances of the calculations.

Table 6. Keywords for prevention of chemical reactions

Keyword

  

Description

stop_rxn

0

Do not prevent chemical reactions during geometry optimizations.

 

1

Add repulsive terms if bonds are formed and harmonic constraints if bonds are broken.

 

2

Add repulsive terms if bonds are formed only

 

3

Add harmonic constraints term if bonds are broken only.

stop_rxn_epsilon

35.0

Maximum strength of repulsive potential ε in kcal mol−1 Å2.

stop_rxn_sigma

0.15

Width parameter for repulsive potential σ in Å−2.

stop_rxn_kval

1000.0

Force constant for harmonic restraint k in kcal mol−1 Å−2.

stop_rxn_offset

0.0

Width of flat bottom a in Å.

The keywords shown in Table 7 may be used to specify the geometry convergence criteria. The values may be scaled to five times their default values with the keyword setting iaccg=3 for a quicker, coarser calculation, or to a tenth of the default values for tighter convergence with iaccg=5. The first two keywords in Table 7 have units of hartrees/bohr, gconv5 and gconv6 have units of bohrs, and gconv7 has units of hartrees.

Table 7. Geometry convergence criteria keywords

Keyword

Default value

Convergence Criterion For

gconv1

4.5×10−4

Maximum element of gradient

gconv2

3.0×10−4

rms of gradient elements

gconv5

1.8×10−3

Maximum element of nuclear displacement

gconv6

1.2×10−3

rms of nuclear displacement elements

gconv7

5.0×10−5

Difference between final energies from previous and current geometry optimization iterations

SCF calculations performed for each new structure generated during an optimization are judged to be converged when they meet the criterion for the root mean square of the change in density matrix elements, which is controlled by the keyword dconv; the usual SCF energy convergence criterion (econv) is ignored for optimizations.

If you want to save the structure at each step of a geometry optimization in a Maestro-formatted file, set ip472=2. You can also extract the structures from the output file to a Maestro file with the command

$SCHRODINGER/utilities/jagconvert -ijout jobname.out -omultimae filename.mae

If you import these structures into Maestro, you should set the color scheme manually: it is not set correctly on import.

To calculate certain properties (charges, multipole moments, Fukui indices) at each step in a geometry optimization, set props_each_step=1. This allows you to examine these properties during the course of a geometry optimization for points at which they change significantly.

Geometry Optimization Examples

Note: As in energy calculations, geometry optimizations with default settings are done in gas-phase, in the pseudospectral approximation and with symmetry enabled.

Example input file (opt-default-0001.in):

&gen
igeopt=1
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_default_0001 opt-default-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-default-0001.in
Output files

Note: Only the gradient is calculated. No optimization steps are taken.

Example input file (opt-justgrad-0001.in):

&gen
igeopt=-1
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_justgrad_0001 opt-justgrad-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-justgrad-0001.in
Output files

Note: Setting ip11=2 prints bond-lengths, bond angles, and torsional angles.

Example input file (opt-constrained-0001.in):

&gen
igeopt=1
dftname=b3lyp-d3
basis=6-31G*+
ip11=2
&
&zmat
C1      3.5805150460579   1.0177528698027  -1.9243164118183
C2      3.4908367628946   1.8991834826942  -0.8577327440766
H3      3.8481121834824   1.3615865686319  -2.9132327668003
H4      3.3844036243266  -0.0371368458295  -1.7942759084100
H5      3.2232187913958   1.5535791563670   0.1308336417221
H6      3.6859144706852   2.9543012314815  -0.9857403836680
&
&coord
C1 C2 #
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_constrained_0001 opt-constrained-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-constrained-0001.in
Output files

Note: Jaguar geometry optimizations use redundant internal coordinates by default.

Example input file (opt-zmatwdummy-0001.in):

&gen
igeopt=1
dftname=b3lyp
basis=6-31G*
ip11=2
&
&zmat
H1
C2 H1 d1
N3 C2 d2 H1 a1
N4 C2 d2 N3 a1 H1 180
C5 N3 d3 C2 a2 H1 180.0
C6 N4 d3 C2 a2 H1 180.0
X7 C2 1.0 H1 90.0 N3 -90.0
C8 C2 d4 X7 90.0 H1 180.0
H9 C8 d5 C6 a3 N4 180.0
H10 C6 d6 C8 a4 H9 0.0
H11 C5 d6 C8 a4 H9 0.0
&
&zvar
d1 = 1.09
d2 = 1.33
d3 = 1.33
a1 = 120.0
a2 = 120.0
a3 = 120.0
a4 = 120.0
d4 = 2.75
d5 = 1.09
d6 = 1.09
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_zmatwdummy_0001 opt-zmatwdummy-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-zmatwdummy-0001.in
Output files

Note: Setting iaccg=5 activates tight convergence criteria. It corresponds to 0.1 times the default criteria from Table 7 of the `Geometry Optimization and Transition-State Keywords` page. iaccg=2 corresponds to default convergence criteria.

Example input file (opt-tightconv-0001.in):

&gen
igeopt=1
iaccg=5
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_tightconv_0001 opt-tightconv-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-tightconv-0001.in
Output files

Note: The setting gconv2=1.0e-4 activates a tighter criterion for RMS gradient convergence. The default setting is 3.0e-4.

Example input file (opt-tightconv-0002.in):

&gen
igeopt=1
gconv2=1.0e-4
basis=6-31G**
dftname=B3LYP-D3
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_tightconv_0002 opt-tightconv-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-tightconv-0002.in
Output files

Example input file (opt-inhess-0001.in):

&gen
igeopt=1
dftname=B3LYP-D3
basis=6-31G**
inhess=4
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_inhess_0001 opt-inhess-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-inhess-0001.in
Output files

Example input file (opt_prop-esp-0001.in):

&gen
basis=6-31G**
igeopt=1
icfit=1
dftname=B3LYP-D3
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_prop_esp_0001 opt_prop-esp-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_prop-esp-0001.in
Output files

Note: The comment lines in the input file describe what each ipN keyword is adding to the output file.

Example input file (opt_prop-freq_moreprint-0001.in):

&gen
basis=6-31G**
dftname=B3LYP-D3
igeopt=1
ifreq=1
! gaussian function list for basis set  
ip1=2 
! memory, disk, and i/o information
ip5=2
! detailed timing information
ip6=2
! gaussian function list for derivatives of basis functions
ip8=2
! bond lengths and angles (3,4,5 adds all possible bonds, angles, torsions) 
ip11=2
! connectivity table 
ip12=2
! overlap matrix
ip18=2
! one-electron Hamiltonian  
ip19=2
! all keyword setting including internal ones
ip24=2
! multiple moments in atomic units 
ip25=2 
! geometries in bohr as well as angstroms
ip26=2
! diagonal force constants in internal coords (3,4 is all force constants)
ip192=2
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_prop_freq_moreprint_0001 opt_prop-freq_moreprint-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_prop-freq_moreprint-0001.in
Output files

Example input file (opt_prop-solv_esp-0001.in):

&gen
igeopt=1
icfit=1
solvent=ethanol
isolv=7
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_prop_solv_esp_0001 opt_prop-solv_esp-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_prop-solv_esp-0001.in
Output files

Note: With xTB, all frequency calculations are done numerically with finite-difference of gradients.

Example input file (opt_freq-xtb-0001.in):

&gen
xtb=1
igeopt=1
ifreq=1
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_freq_xtb_0001 opt_freq-xtb-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_freq-xtb-0001.in
Output files

Note: With QRNN, all frequencies calculations are done numerically with finite-difference of gradients.

Example input file (opt_freq-qrnn-0001.in):

&gen
igeopt=1
ifreq=1
qrnn=3
qrnn_solv=1
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_freq_qrnn_0001 opt_freq-qrnn-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_freq-qrnn-0001.in
Output files

Note: The `ifreq=1` keyword provided in the `&gen` section launches a SECOND frequency calculation for the SECOND optimized geometry following perturbation. The Hessian calculation used to check the geometry after the initial optimization is launched by setting `check_min` to `1`.

Example input file (opt_freq-check_min-0001.in):

&gen
igeopt=1
check_min=1
ifreq=1
dftname=B3LYP-D3
basis=6-31G**
ip11=2
isymm=0
&
&zmat
H1
O2 H1 r1
O3 O2 r2 H1 a1
H4 O3 r3 O2 a2 H1 d1
&
&zvar
r1 = 0.94
r2 = 1.45
r3 = 0.94
a1 = 100.6
a2 = 100.6
d1 = 0.0
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_freq_check_min_0001 opt_freq-check_min-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_freq-check_min-0001.in
Output files

Transition State Geometry Optimization Examples

Note: The inhess=4 setting requests the explicit calculation of an initial Hessian. This is not required. However, for reliable convergence of transition-state optimizations, it is highly recommended to start the procedure with an accurate Hessian.

Example input file (opt_ts-default-0001.in):

&gen
igeopt=2
inhess=4
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1            0.0692136180      0.2132816644     -0.3879323240 
C2            1.4720844665      0.2296330313      0.1734604239 
O3            2.2428204464      1.1677738906      0.1309430510 
N4            2.1499220058     -1.2437703044      0.0898551824 
C5            3.5627058603     -1.2437951941     -0.3080475774 
H6            4.0343246067     -2.1845128465     -0.0147401167 
H7           -0.4855722193     -0.6754858693     -0.0829860366 
H8           -0.4514113750      1.0974920377     -0.0186382961 
H9            0.1210183915      0.2689320396     -1.4813556128 
H10           1.5855338582     -1.8961919808     -0.4512488016 
H11           3.6665480964     -1.1009168850     -1.3871598360 
H12           4.0480965526     -0.4072652266      0.1955270219 
O13           1.0996672074     -0.3560287728      1.9259912398 
H14           1.8663029436     -1.2303195726      1.2206894514 
H15           1.6407504151      0.2556717461      2.4468241668 
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_default_0001 opt_ts-default-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-default-0001.in
Output files

Example input file (opt_ts-lst-0001.in):

&gen
igeopt=2
iqst=1
basis=6-31G**
dftname=B3LYP-D3
&
entry_name: reactant
&zmat
C1      0.2183000000000   0.2198000000000  -0.5171000000000
C2      1.6171000000000   0.1603000000000   0.0649000000000
O3      2.2489000000000   1.1547000000000   0.3755000000000
N4      2.2588000000000  -1.1023000000000   0.0212000000000
C5      3.5667000000000  -1.1818000000000  -0.6303000000000
H6      4.0512000000000  -2.1268000000000  -0.3716000000000
H7     -0.4157000000000  -0.5937000000000  -0.1597000000000
H8     -0.2405000000000   1.1723000000000  -0.2511000000000
H9      0.2987000000000   0.1576000000000  -1.6097000000000
H10     1.6244000000000  -1.8507000000000  -0.2376000000000
H11     3.5025000000000  -1.1047000000000  -1.7247000000000
H12     4.1808000000000  -0.3612000000000  -0.2580000000000
O13     0.7739000000000  -0.4704000000000   2.1756000000000
H14     1.6301000000000  -0.9058000000000   1.8977000000000
H15     1.0665000000000   0.3259000000000   2.6385000000000
&
entry_name2: product
&zmat2
C1      0.0728000000000   0.3145000000000  -0.4135000000000
C2      1.2540000000000   0.4687000000000   0.5052000000000
O3      2.1169000000000   1.3159000000000   0.4126000000000
N4      2.3144000000000  -1.5776000000000   0.0007000000000
C5      3.6690000000000  -1.4276000000000  -0.5002000000000
H6      4.3859000000000  -2.1896000000000  -0.1509000000000
H7     -0.4034000000000  -0.6586000000000  -0.2986000000000
H8     -0.6565000000000   1.0912000000000  -0.1489000000000
H9      0.3857000000000   0.4691000000000  -1.4453000000000
H10     1.8719000000000  -2.4265000000000  -0.3320000000000
H11     3.6592000000000  -1.4677000000000  -1.5952000000000
H12     4.0472000000000  -0.4425000000000  -0.2090000000000
O13     1.1199000000000  -0.2597000000000   1.6884000000000
H14     2.1162000000000  -1.3719000000000   0.9864000000000
H15     1.5416000000000   0.2826000000000   2.3744000000000
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_lst_0001 opt_ts-lst-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-lst-0001.in
Output files

Example input file (opt_ts-qst-0001.in):

&gen
igeopt=2
iqst=1
itrvec=-5
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1      0.0495980000000   0.2533700000000  -0.3607110000000
C2      1.4197410000000   0.2878870000000   0.2842060000000
O3      2.2207240000000   1.2032400000000   0.2164680000000
N4      2.1467540000000  -1.3358890000000   0.0333660000000
C5      3.5632580000000  -1.2838090000000  -0.3163310000000
H6      4.1158520000000  -2.1250250000000   0.1140940000000
H7     -0.4763550000000  -0.6831700000000  -0.1651180000000
H8     -0.5415720000000   1.0753480000000   0.0506750000000
H9      0.1518600000000   0.4065490000000  -1.4388620000000
H10     1.6081090000000  -1.9865110000000  -0.5310510000000
H11     3.6993010000000  -1.2866820000000  -1.4018320000000
H12     3.9603300000000  -0.3414190000000   0.0702700000000
O13     1.1762500000000  -0.3300010000000   1.7855610000000
H14     1.8708550000000  -1.2482310000000   1.1298150000000
H15     1.6182900000000   0.3172350000000   2.3567090000000
&
entry_name2: reactant
&zmat2
C1      0.2183000000000   0.2197920000000  -0.5170720000000
C2      1.6171140000000   0.1603480000000   0.0649390000000
O3      2.2489110000000   1.1546850000000   0.3754610000000
N4      2.2587850000000  -1.1023090000000   0.0211870000000
C5      3.5667470000000  -1.1818210000000  -0.6303440000000
H6      4.0512400000000  -2.1268260000000  -0.3715750000000
H7     -0.4157050000000  -0.5937250000000  -0.1597090000000
H8     -0.2405490000000   1.1723010000000  -0.2511220000000
H9      0.2987020000000   0.1576110000000  -1.6096780000000
H10     1.6244180000000  -1.8506820000000  -0.2376340000000
H11     3.5025230000000  -1.1047410000000  -1.7246620000000
H12     4.1807810000000  -0.3612210000000  -0.2579850000000
O13     0.7738580000000  -0.4704350000000   2.1755670000000
H14     1.6301480000000  -0.9058390000000   1.8977370000000
H15     1.0664630000000   0.3258540000000   2.6385140000000
&
entry_name3: product
&zmat3
C1      0.0728300000000   0.3145440000000  -0.4134690000000
C2      1.2539580000000   0.4686730000000   0.5052290000000
O3      2.1169230000000   1.3158960000000   0.4126330000000
N4      2.3144340000000  -1.5775530000000   0.0007060000000
C5      3.6689680000000  -1.4275930000000  -0.5002000000000
H6      4.3859260000000  -2.1895890000000  -0.1509490000000
H7     -0.4034160000000  -0.6586410000000  -0.2985600000000
H8     -0.6564980000000   1.0912100000000  -0.1489020000000
H9      0.3857450000000   0.4691010000000  -1.4452860000000
H10     1.8719330000000  -2.4265180000000  -0.3320280000000
H11     3.6591630000000  -1.4676670000000  -1.5951720000000
H12     4.0472370000000  -0.4425370000000  -0.2089700000000
O13     1.1199000000000  -0.2596670000000   1.6884280000000
H14     2.1162020000000  -1.3719070000000   0.9864270000000
H15     1.5415760000000   0.2825940000000   2.3744100000000
&
&connect
C2 O13
N4 H14
C2 N4
O13 H14
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_qst_0001 opt_ts-qst-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-qst-0001.in
Output files

Example input file (opt-mlff-0001.in):

&gen
igeopt=1
mlff=Organic_MPNICE
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run opt-mlff-0001.in -jobname=opt_mlff_0001

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2025-3

Input file: opt-mlff-0001.in
Output files

Note: Periodic boundary condition (PBC) cell vectors are taken from the input .mae file in this example. Only atoms in the cell are optimized, not the cell vectors themselves.

Example input file (opt-mlff-0002.in):

MAEFILE: opt-mlff-0002.mae
&gen
igeopt=1
mlff=Organic_MPNICE
mlff_use_pbc=1
&
entry_name: NPB
&zmat
N 4.830000 1.441000 2.320000    
N 8.716883 -14.677671 4.517000  
C 5.335000 2.572000 1.642000    
C 6.285000 3.385000 2.241000    
C 6.759000 4.506000 1.588000    
C 6.321000 4.884000 0.331000    
C 5.374000 4.054000 -0.244000   
C 4.882000 2.926000 0.389000    
C 5.577000 0.774000 3.309000    
C 4.985000 0.368000 4.481000    
C 5.739000 -0.244000 5.451000   
C 7.083000 -0.431000 5.282000   
C 7.673000 -0.050000 4.114000   
C 6.914000 0.515000 3.120000    
C 3.574000 0.873000 1.945000    
C 2.393000 1.598000 2.147000    
C 2.370000 2.888000 2.724000    
C 1.187000 3.532000 2.919000    
C -0.024000 2.949000 2.551000   
C -0.027000 1.733000 1.994000   
C 1.155000 0.987000 1.788000    
C 1.161000 -0.329000 1.247000   
C 2.327000 -1.000000 1.078000   
C 3.536000 -0.393000 1.421000   
C 8.798883 -13.479671 5.250000  
C 9.185883 -13.454671 6.569000  
C 9.282883 -12.257671 7.241000  
C 8.974883 -11.031671 6.678000  
C 8.600883 -11.082671 5.344000  
C 8.521883 -12.263671 4.652000  
C 7.885883 -14.796671 3.370000  
C 6.589883 -14.306671 3.394000  
C 5.826883 -14.348671 2.244000  
C 6.302883 -14.901671 1.081000  
C 7.576883 -15.414671 1.088000  
C 8.354883 -15.366671 2.216000  
C 9.440883 -15.828671 4.955000  
C 8.773883 -16.939671 5.381000  
C 9.460883 -18.073671 5.829000  
C 10.805883 -18.083671 5.859000 
C 11.542883 -16.961671 5.421000 
C 12.954883 -16.969671 5.433000 
C 13.635883 -15.891671 4.978000 
C 12.970883 -14.772671 4.493000 
C 11.606883 -14.717671 4.469000 
C 10.860883 -15.820671 4.946000 
H 6.605000 3.196000 3.161000    
H 7.428000 5.041000 2.056000    
H 5.035000 4.244000 -1.071000   
H 4.183000 2.367000 -0.083000   
H 4.063000 0.564000 4.648000    
H 5.313000 -0.382000 6.259000   
H 7.629000 -0.847000 5.958000   
H 8.625000 -0.287000 4.011000   
H 7.301000 0.811000 2.331000    
H 3.216000 3.287000 3.024000    
H 1.210000 4.462000 3.267000    
H -0.883000 3.399000 2.620000   
H -0.760000 1.141000 1.654000   
H 0.290000 -0.796000 1.032000   
H 2.285000 -1.936000 0.737000   
H 4.444000 -0.933000 1.328000   
H 9.368883 -14.251671 7.045000  
H 9.506883 -12.286671 8.102000  
H 8.351883 -10.252671 4.906000  
H 8.269883 -12.278671 3.775000  
H 6.253883 -13.883671 4.174000  
H 4.923883 -13.978671 2.218000  
H 5.665883 -14.940671 0.241000  
H 7.880883 -15.880671 0.318000  
H 9.252883 -15.723671 2.183000  
H 7.784883 -16.922671 5.334000  
H 8.929883 -18.846671 6.056000  
H 11.352883 -18.934671 6.120000 
H 13.373883 -17.808671 5.851000 
H 14.643883 -15.965671 5.023000 
H 13.454883 -14.026671 4.139000 
H 11.113883 -13.928671 4.111000 
N 8.315059 9.552835 -2.320000   
N 9.319129 -6.115410 9.575970   
C 7.810059 8.421835 -1.642000    
C 6.860059 7.608835 -2.241000    
C 6.386059 6.487835 -1.588000    
C 6.824059 6.109835 -0.331000    
C 7.771059 6.939835 0.244000     
C 8.263059 8.067835 -0.389000    
C 7.568059 10.219835 -3.309000   
C 8.160059 10.625835 -4.481000  
C 7.406059 11.237835 -5.451000  
C 6.062059 11.424835 -5.282000  
C 5.472059 11.043835 -4.114000  
C 6.231059 10.478835 -3.120000  
C 9.571059 10.120835 -1.945000  
C 10.752059 9.395835 -2.147000  
C 10.775059 8.105835 -2.724000  
C 11.958059 7.461835 -2.919000  
C 13.169059 8.044835 -2.551000  
C 13.172059 9.260835 -1.994000  
C 11.990059 10.006835 -1.788000 
C  11.984059 11.322835 -1.247000
C  10.818059 11.993835 -1.078000
C  9.609059 11.386835 -1.421000 
C  9.237129 -7.313410 8.842970  
C  8.850129 -7.338410 7.523970  
C  8.753129 -8.535410 6.851970  
C  9.061129 -9.761410 7.414970  
C  9.435129 -9.710410 8.748970  
C  9.514129 -8.529410 9.440970  
C  10.150129 -5.996410 10.722970
C  11.446129 -6.486410 10.698970
C  12.209129 -6.444410 11.848970
C  11.733129 -5.891410 13.011970
C  10.459129 -5.378410 13.004970
C  9.681129 -5.426410 11.876970 
C  8.595129 -4.964410 9.137970  
C  9.262129 -3.853410 8.711970  
C   8.575129 -2.719410 8.263970
C  7.230129 -2.709410 8.233970  
C  6.493129 -3.831410 8.671970  
C  5.081129 -3.823410 8.659970  
C  4.400129 -4.901410 9.114970  
C  5.065129 -6.020410 9.599970  
C 6.429129 -6.075410 9.623970   
C 7.175129 -4.972410 9.146970   
H 6.540059 7.797835 -3.161000   
H 5.717059 5.952835 -2.056000   
H 8.110059 6.749835 1.071000    
H 8.962059 8.626835 0.083000    
H 9.082059 10.429835 -4.648000  
H 7.832059 11.375835 -6.259000  
H 5.516059 11.840835 -5.958000  
H 4.520059 11.280835 -4.011000  
H 5.844059 10.182835 -2.331000  
H 9.929059 7.706835 -3.024000   
H 11.935059 6.531835 -3.267000  
H 14.028059 7.594835 -2.620000  
H 13.905059 9.852835 -1.654000  
H 12.855059 11.789835 -1.032000 
H 10.860059 12.929835 -0.737000 
H 8.701059 11.926835 -1.328000  
H 8.667129 -6.541410 7.047970   
H 8.529129 -8.506410 5.990970   
H 9.684129 -10.540410 9.186970  
H 9.766129 -8.514410 10.317970  
H 11.782129 -6.909410 9.918970  
H 13.112129 -6.814410 11.874970 
H 12.370129 -5.852410 13.851970 
H 10.155129 -4.912410 13.774970 
H 8.783129 -5.069410 11.909970  
H 10.251129 -3.870410 8.758970  
H 9.106129 -1.946410 8.036970   
H 6.683129 -1.858410 7.972970   
H 4.662129 -2.984410 8.241970   
H 3.392129 -4.827410 9.069970   
H 4.581129 -6.766410 9.953970   
H 6.922129 -6.864410 9.981970   
&

Example input structure file (opt-mlff-0002.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_Source_File_Index
 i_pdb_PDB_CRYST1_z
 r_pdb_PDB_CRYST1_a
 r_pdb_PDB_CRYST1_alpha
 r_pdb_PDB_CRYST1_b
 r_pdb_PDB_CRYST1_beta
 r_pdb_PDB_CRYST1_c
 r_pdb_PDB_CRYST1_gamma
 s_pdb_PDB_CRYST1_Space_Group
 s_pdb_PDB_format_version
 i_m_ct_format
 :::
 NPB 
 1
 1
 10.308
 82.34
 11.354
 77.66
 14.478
 75.53
 "P -1" 
 3.0 
  2
 m_atom[156] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_residue_number
  i_m_color
  s_m_pdb_residue_name
  s_m_pdb_atom_name
  i_m_atomic_number
  i_m_representation
  s_m_color_rgb
  s_m_atom_name
  b_matsci_ASU_Atom
  i_m_pdb_convert_problem
  i_pdb_PDB_serial
  r_m_pdb_occupancy
  :::
  1 26 4.830000 1.441000 2.320000 1 38 "LIG " " N  " 7 3 2E2EFF  N1  1 4 1 1
  2 26 8.716883 -14.677671 4.517000 2 38 "LIG " " N  " 7 3 2E2EFF  N2  1 4 2 1
  3 4 5.335000 2.572000 1.642000 1 24 "LIG " " C  " 6 3 808080  C3  1 4 3 1
  4 4 6.285000 3.385000 2.241000 1 24 "LIG " " C  " 6 3 808080  C4  1 4 4 1
  5 4 6.759000 4.506000 1.588000 1 24 "LIG " " C  " 6 3 808080  C5  1 4 5 1
  6 5 6.321000 4.884000 0.331000 1 24 "LIG " " C  " 6 3 808080  C6  1 4 6 1
  7 4 5.374000 4.054000 -0.244000 1 24 "LIG " " C  " 6 3 808080  C7  1 4 7 1
  8 4 4.882000 2.926000 0.389000 1 24 "LIG " " C  " 6 3 808080  C8  1 4 8 1
  9 4 5.577000 0.774000 3.309000 1 24 "LIG " " C  " 6 3 808080  C9  1 4 9 1
  10 4 4.985000 0.368000 4.481000 1 24 "LIG " " C  " 6 3 808080  C10  1 4 10 1
  11 4 5.739000 -0.244000 5.451000 1 24 "LIG " " C  " 6 3 808080  C11  1 4 11 1
  12 4 7.083000 -0.431000 5.282000 1 24 "LIG " " C  " 6 3 808080  C12  1 4 12 1
  13 4 7.673000 -0.050000 4.114000 1 24 "LIG " " C  " 6 3 808080  C13  1 4 13 1
  14 4 6.914000 0.515000 3.120000 1 24 "LIG " " C  " 6 3 808080  C14  1 4 14 1
  15 4 3.574000 0.873000 1.945000 1 24 "LIG " " C  " 6 3 808080  C15  1 4 15 1
  16 4 2.393000 1.598000 2.147000 1 24 "LIG " " C  " 6 3 808080  C16  1 4 16 1
  17 4 2.370000 2.888000 2.724000 1 24 "LIG " " C  " 6 3 808080  C17  1 4 17 1
  18 4 1.187000 3.532000 2.919000 1 24 "LIG " " C  " 6 3 808080  C18  1 4 18 1
  19 4 -0.024000 2.949000 2.551000 1 24 "LIG " " C  " 6 3 808080  C19  1 4 19 1
  20 4 -0.027000 1.733000 1.994000 1 24 "LIG " " C  " 6 3 808080  C20  1 4 20 1
  21 4 1.155000 0.987000 1.788000 1 24 "LIG " " C  " 6 3 808080  C21  1 4 21 1
  22 4 1.161000 -0.329000 1.247000 1 24 "LIG " " C  " 6 3 808080  C22  1 4 22 1
  23 4 2.327000 -1.000000 1.078000 1 24 "LIG " " C  " 6 3 808080  C23  1 4 23 1
  24 4 3.536000 -0.393000 1.421000 1 24 "LIG " " C  " 6 3 808080  C24  1 4 24 1
  25 4 8.798883 -13.479671 5.250000 2 24 "LIG " " C  " 6 3 808080  C25  1 4 25 1
  26 4 9.185883 -13.454671 6.569000 2 24 "LIG " " C  " 6 3 808080  C26  1 4 26 1
  27 4 9.282883 -12.257671 7.241000 2 24 "LIG " " C  " 6 3 808080  C27  1 4 27 1
  28 5 8.974883 -11.031671 6.678000 2 24 "LIG " " C  " 6 3 808080  C28  1 4 28 1
  29 4 8.600883 -11.082671 5.344000 2 24 "LIG " " C  " 6 3 808080  C29  1 4 29 1
  30 4 8.521883 -12.263671 4.652000 2 24 "LIG " " C  " 6 3 808080  C30  1 4 30 1
  31 4 7.885883 -14.796671 3.370000 2 24 "LIG " " C  " 6 3 808080  C31  1 4 31 1
  32 4 6.589883 -14.306671 3.394000 2 24 "LIG " " C  " 6 3 808080  C32  1 4 32 1
  33 4 5.826883 -14.348671 2.244000 2 24 "LIG " " C  " 6 3 808080  C33  1 4 33 1
  34 4 6.302883 -14.901671 1.081000 2 24 "LIG " " C  " 6 3 808080  C34  1 4 34 1
  35 4 7.576883 -15.414671 1.088000 2 24 "LIG " " C  " 6 3 808080  C35  1 4 35 1
  36 4 8.354883 -15.366671 2.216000 2 24 "LIG " " C  " 6 3 808080  C36  1 4 36 1
  37 4 9.440883 -15.828671 4.955000 2 24 "LIG " " C  " 6 3 808080  C37  1 4 37 1
  38 4 8.773883 -16.939671 5.381000 2 24 "LIG " " C  " 6 3 808080  C38  1 4 38 1
  39 4 9.460883 -18.073671 5.829000 2 24 "LIG " " C  " 6 3 808080  C39  1 4 39 1
  40 4 10.805883 -18.083671 5.859000 2 24 "LIG " " C  " 6 3 808080  C40  1 4 40 1
  41 4 11.542883 -16.961671 5.421000 2 24 "LIG " " C  " 6 3 808080  C41  1 4 41 1
  42 4 12.954883 -16.969671 5.433000 2 24 "LIG " " C  " 6 3 808080  C42  1 4 42 1
  43 4 13.635883 -15.891671 4.978000 2 24 "LIG " " C  " 6 3 808080  C43  1 4 43 1
  44 4 12.970883 -14.772671 4.493000 2 24 "LIG " " C  " 6 3 808080  C44  1 4 44 1
  45 4 11.606883 -14.717671 4.469000 2 24 "LIG " " C  " 6 3 808080  C45  1 4 45 1
  46 4 10.860883 -15.820671 4.946000 2 24 "LIG " " C  " 6 3 808080  C46  1 4 46 1
  47 41 6.605000 3.196000 3.161000 1 21 "LIG " " H  " 1 3 FFFFFF  H47  1 4 47 1
  48 41 7.428000 5.041000 2.056000 1 21 "LIG " " H  " 1 3 FFFFFF  H48  1 4 48 1
  49 41 5.035000 4.244000 -1.071000 1 21 "LIG " " H  " 1 3 FFFFFF  H49  1 4 49 1
  50 41 4.183000 2.367000 -0.083000 1 21 "LIG " " H  " 1 3 FFFFFF  H50  1 4 50 1
  51 41 4.063000 0.564000 4.648000 1 21 "LIG " " H  " 1 3 FFFFFF  H51  1 4 51 1
  52 41 5.313000 -0.382000 6.259000 1 21 "LIG " " H  " 1 3 FFFFFF  H52  1 4 52 1
  53 41 7.629000 -0.847000 5.958000 1 21 "LIG " " H  " 1 3 FFFFFF  H53  1 4 53 1
  54 41 8.625000 -0.287000 4.011000 1 21 "LIG " " H  " 1 3 FFFFFF  H54  1 4 54 1
  55 41 7.301000 0.811000 2.331000 1 21 "LIG " " H  " 1 3 FFFFFF  H55  1 4 55 1
  56 41 3.216000 3.287000 3.024000 1 21 "LIG " " H  " 1 3 FFFFFF  H56  1 4 56 1
  57 41 1.210000 4.462000 3.267000 1 21 "LIG " " H  " 1 3 FFFFFF  H57  1 4 57 1
  58 41 -0.883000 3.399000 2.620000 1 21 "LIG " " H  " 1 3 FFFFFF  H58  1 4 58 1
  59 41 -0.760000 1.141000 1.654000 1 21 "LIG " " H  " 1 3 FFFFFF  H59  1 4 59 1
  60 41 0.290000 -0.796000 1.032000 1 21 "LIG " " H  " 1 3 FFFFFF  H60  1 4 60 1
  61 41 2.285000 -1.936000 0.737000 1 21 "LIG " " H  " 1 3 FFFFFF  H61  1 4 61 1
  62 41 4.444000 -0.933000 1.328000 1 21 "LIG " " H  " 1 3 FFFFFF  H62  1 4 62 1
  63 41 9.368883 -14.251671 7.045000 2 21 "LIG " " H  " 1 3 FFFFFF  H63  1 4 63 1
  64 41 9.506883 -12.286671 8.102000 2 21 "LIG " " H  " 1 3 FFFFFF  H64  1 4 64 1
  65 41 8.351883 -10.252671 4.906000 2 21 "LIG " " H  " 1 3 FFFFFF  H65  1 4 65 1
  66 41 8.269883 -12.278671 3.775000 2 21 "LIG " " H  " 1 3 FFFFFF  H66  1 4 66 1
  67 41 6.253883 -13.883671 4.174000 2 21 "LIG " " H  " 1 3 FFFFFF  H67  1 4 67 1
  68 41 4.923883 -13.978671 2.218000 2 21 "LIG " " H  " 1 3 FFFFFF  H68  1 4 68 1
  69 41 5.665883 -14.940671 0.241000 2 21 "LIG " " H  " 1 3 FFFFFF  H69  1 4 69 1
  70 41 7.880883 -15.880671 0.318000 2 21 "LIG " " H  " 1 3 FFFFFF  H70  1 4 70 1
  71 41 9.252883 -15.723671 2.183000 2 21 "LIG " " H  " 1 3 FFFFFF  H71  1 4 71 1
  72 41 7.784883 -16.922671 5.334000 2 21 "LIG " " H  " 1 3 FFFFFF  H72  1 4 72 1
  73 41 8.929883 -18.846671 6.056000 2 21 "LIG " " H  " 1 3 FFFFFF  H73  1 4 73 1
  74 41 11.352883 -18.934671 6.120000 2 21 "LIG " " H  " 1 3 FFFFFF  H74  1 4 74 1
  75 41 13.373883 -17.808671 5.851000 2 21 "LIG " " H  " 1 3 FFFFFF  H75  1 4 75 1
  76 41 14.643883 -15.965671 5.023000 2 21 "LIG " " H  " 1 3 FFFFFF  H76  1 4 76 1
  77 41 13.454883 -14.026671 4.139000 2 21 "LIG " " H  " 1 3 FFFFFF  H77  1 4 77 1
  78 41 11.113883 -13.928671 4.111000 2 21 "LIG " " H  " 1 3 FFFFFF  H78  1 4 78 1
  79 26 8.315059 9.552835 -2.320000 1 38 "LIG " " N  " 7 3 2E2EFF  N1  0 4 1 1
  80 26 9.319129 -6.115410 9.575970 2 38 "LIG " " N  " 7 3 2E2EFF  N2  0 4 2 1
  81 4 7.810059 8.421835 -1.642000 1 24 "LIG " " C  " 6 3 808080  C3  0 4 3 1
  82 4 6.860059 7.608835 -2.241000 1 24 "LIG " " C  " 6 3 808080  C4  0 4 4 1
  83 4 6.386059 6.487835 -1.588000 1 24 "LIG " " C  " 6 3 808080  C5  0 4 5 1
  84 5 6.824059 6.109835 -0.331000 1 24 "LIG " " C  " 6 3 808080  C6  0 4 6 1
  85 4 7.771059 6.939835 0.244000 1 24 "LIG " " C  " 6 3 808080  C7  0 4 7 1
  86 4 8.263059 8.067835 -0.389000 1 24 "LIG " " C  " 6 3 808080  C8  0 4 8 1
  87 4 7.568059 10.219835 -3.309000 1 24 "LIG " " C  " 6 3 808080  C9  0 4 9 1
  88 4 8.160059 10.625835 -4.481000 1 24 "LIG " " C  " 6 3 808080  C10  0 4 10 1
  89 4 7.406059 11.237835 -5.451000 1 24 "LIG " " C  " 6 3 808080  C11  0 4 11 1
  90 4 6.062059 11.424835 -5.282000 1 24 "LIG " " C  " 6 3 808080  C12  0 4 12 1
  91 4 5.472059 11.043835 -4.114000 1 24 "LIG " " C  " 6 3 808080  C13  0 4 13 1
  92 4 6.231059 10.478835 -3.120000 1 24 "LIG " " C  " 6 3 808080  C14  0 4 14 1
  93 4 9.571059 10.120835 -1.945000 1 24 "LIG " " C  " 6 3 808080  C15  0 4 15 1
  94 4 10.752059 9.395835 -2.147000 1 24 "LIG " " C  " 6 3 808080  C16  0 4 16 1
  95 4 10.775059 8.105835 -2.724000 1 24 "LIG " " C  " 6 3 808080  C17  0 4 17 1
  96 4 11.958059 7.461835 -2.919000 1 24 "LIG " " C  " 6 3 808080  C18  0 4 18 1
  97 4 13.169059 8.044835 -2.551000 1 24 "LIG " " C  " 6 3 808080  C19  0 4 19 1
  98 4 13.172059 9.260835 -1.994000 1 24 "LIG " " C  " 6 3 808080  C20  0 4 20 1
  99 4 11.990059 10.006835 -1.788000 1 24 "LIG " " C  " 6 3 808080  C21  0 4 21 1
  100 4 11.984059 11.322835 -1.247000 1 24 "LIG " " C  " 6 3 808080  C22  0 4 22 1
  101 4 10.818059 11.993835 -1.078000 1 24 "LIG " " C  " 6 3 808080  C23  0 4 23 1
  102 4 9.609059 11.386835 -1.421000 1 24 "LIG " " C  " 6 3 808080  C24  0 4 24 1
  103 4 9.237129 -7.313410 8.842970 2 24 "LIG " " C  " 6 3 808080  C25  0 4 25 1
  104 4 8.850129 -7.338410 7.523970 2 24 "LIG " " C  " 6 3 808080  C26  0 4 26 1
  105 4 8.753129 -8.535410 6.851970 2 24 "LIG " " C  " 6 3 808080  C27  0 4 27 1
  106 5 9.061129 -9.761410 7.414970 2 24 "LIG " " C  " 6 3 808080  C28  0 4 28 1
  107 4 9.435129 -9.710410 8.748970 2 24 "LIG " " C  " 6 3 808080  C29  0 4 29 1
  108 4 9.514129 -8.529410 9.440970 2 24 "LIG " " C  " 6 3 808080  C30  0 4 30 1
  109 4 10.150129 -5.996410 10.722970 2 24 "LIG " " C  " 6 3 808080  C31  0 4 31 1
  110 4 11.446129 -6.486410 10.698970 2 24 "LIG " " C  " 6 3 808080  C32  0 4 32 1
  111 4 12.209129 -6.444410 11.848970 2 24 "LIG " " C  " 6 3 808080  C33  0 4 33 1
  112 4 11.733129 -5.891410 13.011970 2 24 "LIG " " C  " 6 3 808080  C34  0 4 34 1
  113 4 10.459129 -5.378410 13.004970 2 24 "LIG " " C  " 6 3 808080  C35  0 4 35 1
  114 4 9.681129 -5.426410 11.876970 2 24 "LIG " " C  " 6 3 808080  C36  0 4 36 1
  115 4 8.595129 -4.964410 9.137970 2 24 "LIG " " C  " 6 3 808080  C37  0 4 37 1
  116 4 9.262129 -3.853410 8.711970 2 24 "LIG " " C  " 6 3 808080  C38  0 4 38 1
  117 4 8.575129 -2.719410 8.263970 2 24 "LIG " " C  " 6 3 808080  C39  0 4 39 1
  118 4 7.230129 -2.709410 8.233970 2 24 "LIG " " C  " 6 3 808080  C40  0 4 40 1
  119 4 6.493129 -3.831410 8.671970 2 24 "LIG " " C  " 6 3 808080  C41  0 4 41 1
  120 4 5.081129 -3.823410 8.659970 2 24 "LIG " " C  " 6 3 808080  C42  0 4 42 1
  121 4 4.400129 -4.901410 9.114970 2 24 "LIG " " C  " 6 3 808080  C43  0 4 43 1
  122 4 5.065129 -6.020410 9.599970 2 24 "LIG " " C  " 6 3 808080  C44  0 4 44 1
  123 4 6.429129 -6.075410 9.623970 2 24 "LIG " " C  " 6 3 808080  C45  0 4 45 1
  124 4 7.175129 -4.972410 9.146970 2 24 "LIG " " C  " 6 3 808080  C46  0 4 46 1
  125 41 6.540059 7.797835 -3.161000 1 21 "LIG " " H  " 1 3 FFFFFF  H47  0 4 47 1
  126 41 5.717059 5.952835 -2.056000 1 21 "LIG " " H  " 1 3 FFFFFF  H48  0 4 48 1
  127 41 8.110059 6.749835 1.071000 1 21 "LIG " " H  " 1 3 FFFFFF  H49  0 4 49 1
  128 41 8.962059 8.626835 0.083000 1 21 "LIG " " H  " 1 3 FFFFFF  H50  0 4 50 1
  129 41 9.082059 10.429835 -4.648000 1 21 "LIG " " H  " 1 3 FFFFFF  H51  0 4 51 1
  130 41 7.832059 11.375835 -6.259000 1 21 "LIG " " H  " 1 3 FFFFFF  H52  0 4 52 1
  131 41 5.516059 11.840835 -5.958000 1 21 "LIG " " H  " 1 3 FFFFFF  H53  0 4 53 1
  132 41 4.520059 11.280835 -4.011000 1 21 "LIG " " H  " 1 3 FFFFFF  H54  0 4 54 1
  133 41 5.844059 10.182835 -2.331000 1 21 "LIG " " H  " 1 3 FFFFFF  H55  0 4 55 1
  134 41 9.929059 7.706835 -3.024000 1 21 "LIG " " H  " 1 3 FFFFFF  H56  0 4 56 1
  135 41 11.935059 6.531835 -3.267000 1 21 "LIG " " H  " 1 3 FFFFFF  H57  0 4 57 1
  136 41 14.028059 7.594835 -2.620000 1 21 "LIG " " H  " 1 3 FFFFFF  H58  0 4 58 1
  137 41 13.905059 9.852835 -1.654000 1 21 "LIG " " H  " 1 3 FFFFFF  H59  0 4 59 1
  138 41 12.855059 11.789835 -1.032000 1 21 "LIG " " H  " 1 3 FFFFFF  H60  0 4 60 1
  139 41 10.860059 12.929835 -0.737000 1 21 "LIG " " H  " 1 3 FFFFFF  H61  0 4 61 1
  140 41 8.701059 11.926835 -1.328000 1 21 "LIG " " H  " 1 3 FFFFFF  H62  0 4 62 1
  141 41 8.667129 -6.541410 7.047970 2 21 "LIG " " H  " 1 3 FFFFFF  H63  0 4 63 1
  142 41 8.529129 -8.506410 5.990970 2 21 "LIG " " H  " 1 3 FFFFFF  H64  0 4 64 1
  143 41 9.684129 -10.540410 9.186970 2 21 "LIG " " H  " 1 3 FFFFFF  H65  0 4 65 1
  144 41 9.766129 -8.514410 10.317970 2 21 "LIG " " H  " 1 3 FFFFFF  H66  0 4 66 1
  145 41 11.782129 -6.909410 9.918970 2 21 "LIG " " H  " 1 3 FFFFFF  H67  0 4 67 1
  146 41 13.112129 -6.814410 11.874970 2 21 "LIG " " H  " 1 3 FFFFFF  H68  0 4 68 1
  147 41 12.370129 -5.852410 13.851970 2 21 "LIG " " H  " 1 3 FFFFFF  H69  0 4 69 1
  148 41 10.155129 -4.912410 13.774970 2 21 "LIG " " H  " 1 3 FFFFFF  H70  0 4 70 1
  149 41 8.783129 -5.069410 11.909970 2 21 "LIG " " H  " 1 3 FFFFFF  H71  0 4 71 1
  150 41 10.251129 -3.870410 8.758970 2 21 "LIG " " H  " 1 3 FFFFFF  H72  0 4 72 1
  151 41 9.106129 -1.946410 8.036970 2 21 "LIG " " H  " 1 3 FFFFFF  H73  0 4 73 1
  152 41 6.683129 -1.858410 7.972970 2 21 "LIG " " H  " 1 3 FFFFFF  H74  0 4 74 1
  153 41 4.662129 -2.984410 8.241970 2 21 "LIG " " H  " 1 3 FFFFFF  H75  0 4 75 1
  154 41 3.392129 -4.827410 9.069970 2 21 "LIG " " H  " 1 3 FFFFFF  H76  0 4 76 1
  155 41 4.581129 -6.766410 9.953970 2 21 "LIG " " H  " 1 3 FFFFFF  H77  0 4 77 1
  156 41 6.922129 -6.864410 9.981970 2 21 "LIG " " H  " 1 3 FFFFFF  H78  0 4 78 1
  :::
 } 
 m_bond[170] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  i_m_from_rep
  i_m_to_rep
  :::
  1 1 9 1 3 3
  2 1 3 1 3 3
  3 1 15 1 3 3
  4 2 25 1 3 3
  5 2 31 1 3 3
  6 2 37 1 3 3
  7 3 8 1 3 3
  8 3 4 1 3 3
  9 4 47 1 3 3
  10 4 5 1 3 3
  11 5 48 1 3 3
  12 5 6 1 3 3
  13 6 7 1 3 3
  14 6 84 1 3 3
  15 7 49 1 3 3
  16 7 8 1 3 3
  17 8 50 1 3 3
  18 9 10 1 3 3
  19 9 14 1 3 3
  20 10 51 1 3 3
  21 10 11 1 3 3
  22 11 52 1 3 3
  23 11 12 1 3 3
  24 12 53 1 3 3
  25 12 13 1 3 3
  26 13 54 1 3 3
  27 13 14 1 3 3
  28 14 55 1 3 3
  29 15 24 1 3 3
  30 15 16 1 3 3
  31 16 17 1 3 3
  32 16 21 1 3 3
  33 17 56 1 3 3
  34 17 18 1 3 3
  35 18 57 1 3 3
  36 18 19 1 3 3
  37 19 58 1 3 3
  38 19 20 1 3 3
  39 20 59 1 3 3
  40 20 21 1 3 3
  41 21 22 1 3 3
  42 22 60 1 3 3
  43 22 23 1 3 3
  44 23 61 1 3 3
  45 23 24 1 3 3
  46 24 62 1 3 3
  47 25 26 1 3 3
  48 25 30 1 3 3
  49 26 63 1 3 3
  50 26 27 1 3 3
  51 27 64 1 3 3
  52 27 28 1 3 3
  53 28 29 1 3 3
  54 28 106 1 3 3
  55 29 65 1 3 3
  56 29 30 1 3 3
  57 30 66 1 3 3
  58 31 36 1 3 3
  59 31 32 1 3 3
  60 32 67 1 3 3
  61 32 33 1 3 3
  62 33 68 1 3 3
  63 33 34 1 3 3
  64 34 69 1 3 3
  65 34 35 1 3 3
  66 35 70 1 3 3
  67 35 36 1 3 3
  68 36 71 1 3 3
  69 37 38 1 3 3
  70 37 46 1 3 3
  71 38 72 1 3 3
  72 38 39 1 3 3
  73 39 73 1 3 3
  74 39 40 1 3 3
  75 40 74 1 3 3
  76 40 41 1 3 3
  77 41 46 1 3 3
  78 41 42 1 3 3
  79 42 75 1 3 3
  80 42 43 1 3 3
  81 43 76 1 3 3
  82 43 44 1 3 3
  83 44 77 1 3 3
  84 44 45 1 3 3
  85 45 78 1 3 3
  86 45 46 1 3 3
  87 79 87 1 3 3
  88 79 81 1 3 3
  89 79 93 1 3 3
  90 80 103 1 3 3
  91 80 109 1 3 3
  92 80 115 1 3 3
  93 81 86 1 3 3
  94 81 82 1 3 3
  95 82 125 1 3 3
  96 82 83 1 3 3
  97 83 126 1 3 3
  98 83 84 1 3 3
  99 84 85 1 3 3
  100 85 127 1 3 3
  101 85 86 1 3 3
  102 86 128 1 3 3
  103 87 88 1 3 3
  104 87 92 1 3 3
  105 88 129 1 3 3
  106 88 89 1 3 3
  107 89 130 1 3 3
  108 89 90 1 3 3
  109 90 131 1 3 3
  110 90 91 1 3 3
  111 91 132 1 3 3
  112 91 92 1 3 3
  113 92 133 1 3 3
  114 93 102 1 3 3
  115 93 94 1 3 3
  116 94 95 1 3 3
  117 94 99 1 3 3
  118 95 134 1 3 3
  119 95 96 1 3 3
  120 96 135 1 3 3
  121 96 97 1 3 3
  122 97 136 1 3 3
  123 97 98 1 3 3
  124 98 137 1 3 3
  125 98 99 1 3 3
  126 99 100 1 3 3
  127 100 138 1 3 3
  128 100 101 1 3 3
  129 101 139 1 3 3
  130 101 102 1 3 3
  131 102 140 1 3 3
  132 103 104 1 3 3
  133 103 108 1 3 3
  134 104 141 1 3 3
  135 104 105 1 3 3
  136 105 142 1 3 3
  137 105 106 1 3 3
  138 106 107 1 3 3
  139 107 143 1 3 3
  140 107 108 1 3 3
  141 108 144 1 3 3
  142 109 114 1 3 3
  143 109 110 1 3 3
  144 110 145 1 3 3
  145 110 111 1 3 3
  146 111 146 1 3 3
  147 111 112 1 3 3
  148 112 147 1 3 3
  149 112 113 1 3 3
  150 113 148 1 3 3
  151 113 114 1 3 3
  152 114 149 1 3 3
  153 115 116 1 3 3
  154 115 124 1 3 3
  155 116 150 1 3 3
  156 116 117 1 3 3
  157 117 151 1 3 3
  158 117 118 1 3 3
  159 118 152 1 3 3
  160 118 119 1 3 3
  161 119 124 1 3 3
  162 119 120 1 3 3
  163 120 153 1 3 3
  164 120 121 1 3 3
  165 121 154 1 3 3
  166 121 122 1 3 3
  167 122 155 1 3 3
  168 122 123 1 3 3
  169 123 156 1 3 3
  170 123 124 1 3 3
  :::
 } 
}

To submit the job from the command line, download the input files (below) and enter the following command:

$SCHRODINGER/jaguar run opt-mlff-0002.in -jobname=opt_mlff_0002

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2025-3

Input file: opt-mlff-0002.in
Input structure: opt-mlff-0002.mae
Output files

Note: With MPNICE, all frequencies calculations are done numerically with finite-difference of gradients.

Example input file (opt_freq-mlff-0001.in):

&gen
igeopt=1
ifreq=1
mlff=Organic_MPNICE
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run opt_freq-mlff-0001.in -jobname=opt_freq_mlff_0001

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2025-3

Input file: opt_freq-mlff-0001.in
Output files