Files and Subprograms used by Tinker

TINKER is a collection of programs particularly well suited for the construction and manipulation of peptides and oligonucleotides. The programs are the result of many years of work by Jay Ponder and his research group. The program suite operates through the action of various subprograms on a set of files sharing the same principal name (such as testz1), but carrying variable endings depending on the particular purpose and content of the file. The most important files are:

the cartesian coordinate file (.xyz)
This file contains the cartesian coordinates of the system. The atom labels used in this file depend on the force field chosen in the keyword file (see below).

the internal coordinate file (.int)
This file contains the structure of the system in internal coordinates. As for the xyz-coordinate file the atom labels depend on the force field chosen in the keyword file.

the sequence file (.seq)
This file contains the sequence of the peptide (using the three-letter code) or oligonucleotide.

the keyword file (.key)
This file contains additional information such as the force field parameters that should be used during geometry optimization or molecular dynamics calculations of the system.

One general note with respect to the files used by Tinker should be made on file updating. In order to avoid overwriting of existing files, Tinker generates new files in a systematic way in case older files should exist. Should, for example, the coordinate file testz1.xyz exist at the beginning of a geometry optimization, a new file named testz1.xyz_2 will be generated containing the optimized coordinates. Repeated execution of the optimization program with increasingly accurate convergence criteria will generate the files testz1.xyz_3, testz1.xyz_4 and so on. On startup the Tinker programs will therefore search for the file with the highest version number and use this file for input.

The programs of the Tinker suite are all located in the directory /usr/local/tinker/bin. In order to start the programs from the tcsh command line interface, you should add the following line to your .cshrc file:

set path = ( /usr/local/tinker /usr/local/tinker/bin $path)

Also, in order to organize the Java environment used by Tinker and FFE appropriately, check whether either the file libjvm.so exists in the directory /usr/lib, or whether a link has been set to point to the corresponding location in the Tinker directory such as:

libjvm.so -> /usr/local/tinker/jre/lib/i386/client/libjvm.so

The most important subprograms of the program suite are:
 

structure generation and manipulation

protein
This subprogram builds up peptide chains and generates the corresponding coordinate files (.xyz and .int) and the sequence file (.seq).

archive
This program takes a number of single coordinate files (in xyz format) and produces one large file containing all the structures. The program can also be used to extract single structures out of existing archives.

intxyz
A program for the interconversion of internal and cartesian coordinates. If invoked with intxyz testz1 the program reads the internal coordinates from file testz1.int and writes out the cartesian coordinates to file testz1.xyz. The conversion of cartesian to internal coordinates can analogously be performed using the program xyzint.
 

structure optimization

minimize
This is a gradient minimizer requiring only the energy and the gradient in order to optimize the structure of the system. It is recommend for the preliminary minimization of structures generated by the protein subprogram. The first argument given to the program is the principal name of the system under investigation (such as testz1) and the second argument is the convergence criterion in kcal/mol/angstroms. A criterion of 0.1 may be adequate for preliminary geometry optimization.

newton
This is a geometry optimizer based on a Newton-Raphson algorithm (requiring energy, gradient, and second derivative information) that can also be coached to optimize conformational transition states. As input the program accepts the principal name of the system under investigation, additional information for the particular variant of the algorithm and for preconditioning the system (both of which can be directed with the argument a to assume default values), and finally the convergence criterion (in kcal/mol/angstroms).

optimize
This is a gradient minimizer operating in cartesian coordinate space and requiring calculation of the energy, the gradients, and an approximate second derivative matrix. The first argument given to the program is the principal name of the system under investigation and the second argument is the convergence criterion in kcal/mol/angstrom.
 

conformational search

scan
After initial geometry optimization of the input structure (supplied in a xyz-coordinates file) the program searches the conformational space in a systematic fashion by following low energy torsional modes from one conformational isomer to the next one. After each "hopping" step, the program performs a local geometry optiomization of the structure. The conformational minima found in this way are included in a list of conformers, whose low energy torsional modes are followed in order to find new conformational isomers. In case all modes of all known conformers have been tested without finding new minima, the search is ended. The program accepts as arguments the principal name of the system under study (in order to locate the corresponding xyz-coordinates file), information on the torsional angles included in the search process (0 chooses automatic selection), the number of search directions during the local search (default is 5), the energy threshold for local minima (default is 100.0 kcal/mol), and the convergence criterion for local geometry optimizations (default is 0.0001 kcal/mol/angstrom).

sniffer
This program implements the sniffer global trajectory method for searching for global minima. As input the program accepts the principal name of the system under study in order to locate the xyz-coordinate file used as the seed structure. The subsequent arguments accepted by the program are the number of trial structures (default is 100), the target energy of the system (default is 0.0), and the convergence criterion per atom (default is 1.0).
 

structure characterization

vibrate
This program calculates the vibrational frequency spectrum of the structure described in the input (.xyz) file. As input the program takes the principal file name of the system as well as the number of the vibration, for which displacements are to be written to the output file. The list of vibration numbers is terminated by 0.

superpose
This program predicts the best possible superposition of two structures a and b and calculates the final residual difference d_ab (rms distance) between the structures.