##################################### TEST Directory for the Tinker Package ##################################### This directory contains some test casess illustrating use of several of the programs in the Tinker package. For example, the argon.run file contains commands to run the first test case. The resulting output is found in the file argon.log. The clean.make script will remove any output files generated during these test runs, and should be invoked prior to validating Tinker executables against the provided log files. (1) ANION estimates the hydration free energy difference for Cl- vs. Br- anion via a 10 picosecond simulation of a "hybrid" anion in a box of water, followed by free energy perturbation (2) ARGON minimize, then perform 25 picoseconds of molecular dynamics simulation, on a box with 150 argon atoms (3) CATION estimates the hydration free energy difference for Rb+ vs. Cs+ cation via a 2 picosecond simulation of each cation in a box of water, followed by a BAR free energy calculation (4) CLUSTER performs 10 Gaussian density annealing trials on a cluster of 13 argon atoms to find the global minimum energy structure (5) CRAMBIN generate a Tinker XYZ file from a PDB file, followed by single point energy computation and determination of the molecular volume and surface area (6) CYCLOHEXANE locate the transition state between chair and boat cyclohexane via two methods: the Muller-Brown saddle point method, and path sampling using the Elber algorithm; vibrational analysis of the results shows the same TS with one negative frequency (7) DHFR run 10 molecular dynamics steps on pre-equilibrated DHFR protein in water using the AMOEBA force field (the so-called Joint Amber-CHARMM benchmark) (8) DIALANINE find all local minima of alanine dipeptide via a potential energy surface scan using torsional modes to jump between minima (9) ENKEPHALIN generate coordinates from amino acid sequence and phi/psi angles, followed by energy minimization and determination of the lowest frequency normal mode (10) ETHANOL fit torsional parameter values for the C-C-O-H bond based on relative quantum mechanical (G09) energies for rotating the C-O bond (11) FORMAMIDE generate a unit cell from fractional coordinates, followed by full crystal energy minimization and determination of optimal carbonyl oxygen parameters via a fit to lattice energy and structure (12) GPCR find the lowest-frequency bacteriorhodopsin normal mode using a sliding block iterative diagonalization (alter gpcr.run script to save the file gpcr.001 if you want to view the mode; this example can require up to an hour to complete) (13) HELIX optimize rigid-body packing of two ideal polyalanine helices using only van der Waals interactions (14) ICE short MD simulation of the monoclinic ice V crystal form using the iAMOEBA water model, neighbor lists and PME electrostatics (15) IFABP generate distance geometry structures for intestinal fatty acid binding protein from NOE distances and torsional restraints (16) LIQUID print the system setup and compute the force field energy components for three small liquid water boxes using the AMOEBA, AMOEBA+ and HIPPO force fields (17) METHANOL process distributed multipole analysis (DMA) output to extract coordinates and permanent multipoles, set local frames and polarization groups, modify the intramolecular polarization, and average equivalent atomic sites (18) NITROGEN calculate the self-diffusion constant and N-N radial distribution function for a liquid nitrogen box via analysis of a 50ps MD trajectory (19) POLYALA generate an extended conformation of capped alanine octapeptide, then use Monte Carlo Minimization with torsion moves to find the 3/10 helix global minimum (20) SALT convert sodium chloride asymmetric unit to the unit cell, then minimize the crystal from the diffraction structure using Ewald summation electrostatics (21) VASOPRESSIN compare analytical and finite difference numerical gradient over Cartesian and internal coordinates for vasopressin using the AMOEBA force field model (22) WATER fit the electrostatic potential for TIP3P, AMOEBA and HIPPO water models to a QM-derived potential (MP2/aug-cc-pVTZ) on a grid of points outside the molecular surface