ALCHEMY


ANALYZE


ANNEAL


ARCHIVE


BAR


CORRELATE


CRYSTAL


DIFFUSE


DISTGEOM


DYNAMIC


GDA


INTEDIT


INTXYZ


MINIMIZE


MINIROT


MINIRIGID


MOL2XYZ


MOLXYZ


MONTE


NEWTON


NEWTROT


NUCLEIC


OPTIMIZE


OPTIROT


OPTIRIGID


PATH


PDBXYZ


POLARIZE


POLEDIT


POTENTIAL



PRMEDIT

Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  1
 Reformated Parameter File Written To:  parameter.prm

Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  2
 Renumbered Parameter File Written To:  parameter.prm_2

Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  3
 Enter Starting Number for Atom Types [1] :  1
 Renumbered Parameter File Written To:  parameter.prm_3
 
Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  4
 Enter Starting Number for Atom Classes [1] :  1
 Renumbered Parameter File Written To:  parameter.prm_4
 
Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  5
 Enter Starting Number for Atom Types [1] :  1
 Enter Starting Number for Atom Classes [1] :  2
 Renumbered Parameter File Written To:  parameter.prm_5
 
Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  6
 Sorted Multipole Values Written To:  multipole.prm
 
Enter Potential Parameter File Name :  a.xyz

 The Parameter Editing Facility can Provide :

    (1) Format Individual Parameter Records
    (2) Reorder Individual Parameter Records
    (3) Renumber the Atom Types, and Reorder
    (4) Renumber the Atom Classes, and Reorder
    (5) Renumber Types and Classes, and Reorder
    (6) Sort and Format Multipole Parameters
    (7) Renumber and Format Biotype Parameters

 Enter the Number of the Desired Choice :  7
 Renumbered Biotype Values Written To:  biotype.prm

PROTEIN

Enter Name to be Used for Output Files :  test2
Enter Title :  test2
Enter Potential Parameter File Name :  ../../params/amoeba04

 Enter One Residue Name per Line as the Standard Three-Letter Code, then
 Phi Psi Omega (3F), Chi Angles (4F), then Disulfide Partner if CYX (I),
 and D/L Chirality as Desired (A1)

 If Only Residue Names are Entered, the Default is to Build an Extended
 Conformation Using L-Amino Acids and Zwitterionic Termini

 Regular Amino Acids:  GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, CYX, PRO,
 PHE, TYR, TRP, HIS, ASP, ASN, GLU, GLN, MET, LYS, ARG, ORN, AIB

 Alternative Protonation States:  CYD, TYD, HID, HIE, ASH, GLH, LYD

 N-Terminal Cap Residues:  H2N=Deprotonated, FOR=Formyl, ACE=Acetyl,
                           PCA=Pyroglutamic Acid
 C-Terminal Cap Residues:  COH=Protonated, NH2=Amide, NME=N-MethylAmide

 Use Residue Name=MOL to Start a New Chain, and Use <CR> to End Input

 Enter Residue   1 :  ALA
 Enter Residue   2 :  GLY
 Enter Residue   3 :

 Cyclize the Polypeptide Chain [N] :  N

PSS

Enter Cartesian Coordinate File Name :  a.xyz
Enter the Potential Surface Smoothing Parameter [0.0] :  0.0
Enter the Number of Steps for Smoothing Schedule [100] :  10
Perform Forward Smoothing from Input Structure [Y] :  Y
Use Quadratic, Cubic or Sigmoidal Schedule (Q [C] or S) :  Q
Local Search Type - Cartesian, Torsional or None (C T or [N]) :  C
Enter the Range of Local Search Directions (1=Highest Freq) :  1

PSSRIGID

Enter Cartesian Coordinate File Name :  a.xyz
Enter the Potential Surface Smoothing Parameter [0.0] :  0

PSSROT

Enter Internal Coordinate File Name :  a.xyz
Enter the Potential Surface Smoothing Parameter [0.0] :  0.1

RADIAL

Enter the Coordinate Archive File Name :  a.xyz
Numbers of First & Last Frame and Step Increment :  1 3 1
Enter 1st & 2nd Atom Names or Type Numbers :  N H H H
Enter Maximum Distance to Accumulate [10.0 Ang] :  10
Enter Width of Distance Bins [0.01 Ang] :  0.1
Include Intramolecular Pairs in Distribution [N] :  Y

SADDLE

Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  0
 Number of Torsions Used in Derivative Computation :     1
 Enter the Number Search Directions for Local Search [5] :  5
 Enter the Energy Threshold for Local Minima [100.0] :  100
 Enter RMS Gradient per Atom Criterion [0.0001] :  0.1
 
Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  1
 Enter Atoms in Rotatable Bond    1 :  1 2
 Enter Atoms in Rotatable Bond    1 :
...

Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  2
 Enter Atoms in Frozen Bond    1 :  1 2
 Enter Atoms in Frozen Bond    2 :
 Number of Torsions Used in Derivative Computation :     1
 Enter the Number Search Directions for Local Search [5] :  5
 Enter the Energy Threshold for Local Minima [100.0] :  0.02
 Enter RMS Gradient per Atom Criterion [0.0001] :  0.1

SCAN

Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  0
 Number of Torsions Used in Derivative Computation :     1
 Enter the Number Search Directions for Local Search [5] :  5
 Enter the Energy Threshold for Local Minima [100.0] :  100
 Enter RMS Gradient per Atom Criterion [0.0001] :  0.1
 

Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  1
 Enter Atoms in Rotatable Bond    1 :  1 2
 Enter Atoms in Rotatable Bond    1 :
 ...
 
Enter Cartesian Coordinate File Name :  a.xyz
Selection of Torsional Angles for Rotation :

    0  - Automatic Selection of Torsional Angles
    1  - Manual Selection of Angles to Rotate
    2  - Manual Selection of Angles to Freeze

 Enter the Method of Choice [0] :  2
 Enter Atoms in Frozen Bond    1 :  1 2
 Enter Atoms in Frozen Bond    2 :
 Number of Torsions Used in Derivative Computation :     1
 Enter the Number Search Directions for Local Search [5] :  5
 Enter the Energy Threshold for Local Minima [100.0] :  0.02
 Enter RMS Gradient per Atom Criterion [0.0001] :  0.1

SNIFFER

Enter Cartesian Coordinate File Name :  a.xyz

SPACEFILL

 Enter Cartesian Coordinate File Name :  a.xyz

 Three Types of Area and Volume can be Computed :

    (1) Van der Waals Area and Volume
    (2) Accessible Area and Excluded Volume
    (3) Contact-Reentrant Area and Volume

 Enter the Number of your Choice [1] :  1
 Include the Hydrogen Atoms in Computation [N] :  Y


 Enter Cartesian Coordinate File Name :  a.xyz

 Three Types of Area and Volume can be Computed :

    (1) Van der Waals Area and Volume
    (2) Accessible Area and Excluded Volume
    (3) Contact-Reentrant Area and Volume

 Enter the Number of your Choice [1] :  2
 Enter a Value for the Probe Radius [1.4 Ang] :  1.4
 Include the Hydrogen Atoms in Computation [N] :  Y
 
 
 Enter Cartesian Coordinate File Name :  a.xyz

 Three Types of Area and Volume can be Computed :

    (1) Van der Waals Area and Volume
    (2) Accessible Area and Excluded Volume
    (3) Contact-Reentrant Area and Volume

 Enter the Number of your Choice [1] :  3
 Enter a Value for the Probe Radius [1.4 Ang] :  1.5
 Include the Hydrogen Atoms in Computation [N] :  Y

SPECTRUM

Enter Name of Velocity Autocorrelation File :  a.xyz
Enter Time Step for Autocorrelation Data [1.0 fs] :  1.0

SUPERPOSE

 Enter Cartesian Coordinate File Name :  a.xyz
 Enter Cartesian Coordinate File Name :  a.xyz

 Two Options are Available :  (1) Fit atoms "M" through "N" from structure 1
 to the corresponding atoms of structure 2. Enter "1,M,N" to use this option.
 If "N" is omitted, the fit uses atoms 1 through "M". If both "M" and "N" are
 omitted, the fit uses all atoms; or (2) Individual entry of atom range pairs
 to be used in the fitting procedure.

 Enter an Option (either 1,M,N or 2 [<CR>=1,0,0]) :  1,2,2
 Include Hydrogen Atoms in the Fitting [Y] :  Y
 Use Mass- or Unit-Weighted Coordinates (M or [U]) :  U
 Write Best-Fit Coordinates of 2nd Molecule [N] :  N
 Cutoff Value for Listing RMS Deviations [0.0] :  0.0
 Structure File 1 :  a.xyz
 Structure File 2 :  a.xyz
 
TESTGRAD

Enter Cartesian Coordinate File Name :  a.xyz
Compute the Analytical Gradient Vector [Y] :  Y
Compute the Numerical Gradient Vector [Y] :   Y
Enter Finite Difference Stepsize [ 0.1D-04 Ang] :  0.1

TESTHESS

Enter Cartesian Coordinate File Name :  a.xyz
Compute Analytical Hessian Matrix [Y] :  Y
Compute Numerical Hessian Matrix [Y] :   Y
Numerical Hessian from Gradient or Function [G] :  H
Enter Finite Difference Stepsize [ 0.1D-04 Ang] :  0.1
List Individual Hessian Components [N] :   Y

TESTPAIR

Enter Cartesian Coordinate File Name :  a.xyz
Enter Desired Number of Repetitions [1] :  1

TESTPOL

Enter Cartesian Coordinate File Name :  a.xyz

TESTROT

Enter Internal Coordinate File Name :  a.xyz

TIMER

Enter Cartesian Coordinate File Name :  a.xyz
Enter Desired Number of Repetitions [1] :  1
Include Timing for Hessian Evaluations [N] :  Y

TIMEROT

Enter Internal Coordinate File Name :  a.xyz

TORSFIT

Enter Cartesian Coordinate File Name :  a.xyz
Enter Central Atoms of the 1st Torsion : N
Enter Central Atoms of the 1st Torsion : N
Enter Central Atoms of the 1st Torsion : N
Enter Central Atoms of the 1st Torsion :

VALENCE

The Tinker Valence Parameter Utility Can :

    (1) Set Initial Values for Valence Parameters
    (2) Compare QM and MM Vibrational Frequencies
    (3) Force Fit of Parameters to QM Results
    (4) Structure Fit of Parameters to QM Results

 Enter the Number of the Desired Choice :  1
 Enter Cartesian Coordinate File Name :  a.xyz
 Enter the Name of the Gaussian Output File :  a.out
 Enter the Name of the Gaussian Output File :  a.out
 Enter the Name of the Gaussian Output File :  a.xyz

The Tinker Valence Parameter Utility Can :

    (1) Set Initial Values for Valence Parameters
    (2) Compare QM and MM Vibrational Frequencies
    (3) Force Fit of Parameters to QM Results
    (4) Structure Fit of Parameters to QM Results

 Enter the Number of the Desired Choice :  2
 Enter Cartesian Coordinate File Name :  a.xyz
 Enter the Name of the Gaussian Output File :  a.xyz
 
The Tinker Valence Parameter Utility Can :

    (1) Set Initial Values for Valence Parameters
    (2) Compare QM and MM Vibrational Frequencies
    (3) Force Fit of Parameters to QM Results
    (4) Structure Fit of Parameters to QM Results

 Enter the Number of the Desired Choice :  3
 Enter Cartesian Coordinate File Name :  a.xyz
 Enter the Name of the Gaussian Output File :  a.xyz
 Enter RMS Gradient Termination Criterion [0.01] :  0.1

 The Tinker Valence Parameter Utility Can :

    (1) Set Initial Values for Valence Parameters
    (2) Compare QM and MM Vibrational Frequencies
    (3) Force Fit of Parameters to QM Results
    (4) Structure Fit of Parameters to QM Results

 Enter the Number of the Desired Choice :  4
 Enter Cartesian Coordinate File Name :  a.xyz
 Enter the Name of the Gaussian Output File :  a.xyz

VIBBIG

Enter Cartesian Coordinate File Name :  a.xyz
Start at Lowest or Highest Frequency Normal Mode [L] :  L
Enter Desired Frequency Cutoff in cm-1 [0.0] :  0.1

VIBRATE

Enter Cartesian Coordinate File Name :  a.xyz
Enter Vibrations to Output [List, A=All or <CR>=Exit] :  A

VIBROT

Enter Internal Coordinate File Name :  a.xyz

XTALFIT

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  1
 Enter Parameter Type then Atom Class or Type(s) :  1 N
 Enter Parameter Type then Atom Class or Type(s) :  1 N
 Enter Parameter Type then Atom Class or Type(s) :
 Enter RMS Gradient Termination Criterion [0.1] :  0.1
 Enter Number of Structures to be Used [1] :  1
 Enter Cartesian Coordinate File Name :  a.xyz

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  2
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :
 Enter Number of Structures to be Used [1] :
 Enter Cartesian Coordinate File Name :  a.xyz

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  3
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :
 Enter Number of Structures to be Used [1] :
 Enter Cartesian Coordinate File Name :  a.xyz

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  4
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :
 Enter Number of Structures to be Used [1] :
 Enter Cartesian Coordinate File Name :  a.xyz

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  5
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :
 Enter Number of Structures to be Used [1] :
 Enter Cartesian Coordinate File Name :
 Enter Cartesian Coordinate File Name :  a.xyz

The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  6
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :  0.1
 Enter Number of Structures to be Used [1] :  1
 Enter Cartesian Coordinate File Name :  a.xyz
 
The Following Parameters can be Fit for each Atom Type :

    (1) Van der Waals Atomic Radius
    (2) Van der Waals Well Depth
    (3) Hydrogen Atom Reduction Factor
    (4) Atomic Partial Charge
    (5) Bond Dipole Moment Magnitude
    (6) Bond Dipole Moment Position
    (7) Atomic Polarizability

 Enter Parameter Type then Atom Class or Type(s) :  7
 Enter Parameter Type then Atom Class or Type(s) :  N
 Enter RMS Gradient Termination Criterion [0.1] :  0.1
 Enter Number of Structures to be Used [1] :  1
 Enter Cartesian Coordinate File Name :  a.xyz

 
XTALMIN

Enter Cartesian Coordinate File Name :  a.xyz

XYZEDIT

Enter Cartesian Coordinate File Name :  a.xyz

 The Tinker XYZ File Editing Utility Can :

    (1) Offset the Numbers of the Current Atoms
    (2) Deletion of Individual Specified Atoms
    (3) Deletion of Specified Types of Atoms
    (4) Deletion of Atoms Outside Cutoff Range
    (5) Insertion of Individual Specified Atoms
    (6) Replace Old Atom Type with a New Type
    (7) Assign Connectivities for Linear Chain
    (8) Assign Connectivities Based on Distance
    (9) Convert Units from Bohrs to Angstroms
   (10) Invert thru Origin to Give Mirror Image
   (11) Translate All Atoms by an X,Y,Z-Vector
   (12) Translate Center of Mass to the Origin
   (13) Translate a Specified Atom to the Origin
   (14) Translate and Rotate to Inertial Frame
   (15) Move to Specified Rigid Body Coordinates
   (16) Move Stray Molecules into Periodic Box
   (17) Delete Molecules Outside of Periodic Box
   (18) Append a Second XYZ File to Current One
   (19) Create and Fill a Periodic Boundary Box
   (20) Soak Current Molecule in Box of Solvent

 Number of the Desired Choice [<CR>=Exit] :  1

 Offset used to Renumber the Atoms [0] :  0

XYZINT

Enter Cartesian Coordinate File Name :  a.xyz
Template (T), Dihedrals (D), Manual (M) or Automatic [A] :  t

Enter Cartesian Coordinate File Name :  a.xyz
Template (T), Dihedrals (D), Manual (M) or Automatic [A] :  d

Enter Cartesian Coordinate File Name :  a.xyz
Template (T), Dihedrals (D), Manual (M) or Automatic [A] :  m
Atom Number to be Defined [    1] :  1
Atom Number to be Defined [    2] :  2
Atom Number to be Defined [    3] :
Atom Number to be Defined [    4] :
Choose a Connected Atom (     2     3) :
Specify with Dihedral Angle or Second Bond Angle (D or [B]) :  d
...

Enter Cartesian Coordinate File Name :  a.xyz
Template (T), Dihedrals (D), Manual (M) or Automatic [A] :  a

XYZMOL2

Enter Cartesian Coordinate File Name :  a.xyz

XYZPDB

Enter Cartesian Coordinate File Name :  a.xyz