Presentation on theme: "Molecular modeling tool - TINKER"— Presentation transcript:
1 Molecular modeling tool - TINKER Ka-Lok NgAsia University
2 TINKER This tool is developed by Prof. Jay Ponder Download the window version of TINKER (Installation Kit for Windows), install itDownload the user's Guide, read the Force Field Explorer (FFE) web page go to documentation page, read the FFE ManualDocuments are also available at C:\Program Files\TINKER\docOpen the FFE
3 Description of Force Field Explorer Components Molecular TreeThe Molecular Tree is a structural hierarchy of each system, used for navigating and making selections. When Force Field Explorer opens a structure file, it attempts to groups atoms into protein/nucleic acid macromolecules and their constituent residues. It also groups ions, water and hetero molecules together. This is done even in the absence of a TINKER sequence file. When a display or color command is chosen, all currently selected groups of atoms are affected.Go to C:\Program Files\TINKER\test, open the enkephalin,xyz file
4 Description of Force Field Explorer Components The first residue of enkephalin has been selected in the Tree view and is highlighted (according to the CPK) model in the graphics window.CPK – after Corey, Pauling and Kultun, N=blue, O=red, C=dark grey, S = yellow, H=light grey
5 Description of Force Field Explorer Components 3D Graphics and Global AxisLeft-clicking the Global Axis, then dragging performs a rotation about the origin of the entire scene. This is useful for manual docking of two systems.Right-clicking the Global Axis, then dragging performs a translation of the entire scene.
6 Description of Force Field Explorer Components Keyword EditorThe Keyword Editor allows modification of keyword files that control various aspects of TINKER calculations. If a Modeling Command is executed on a system, the corresponding Keyword File is automatically saved. Modifications can also be saved at any time using one of the save buttons. Any text or keywords that Force Field Explorer does not recognize are considered “Comments” and are appended to the end of saved key files. As an example, the enkephalin keyword control file is shown below.The Keyword Editor is displaying the enkephalin keyword file.
7 Description of Force Field Explorer Components Modeling CommandsThe Modeling Commands panel of Force Field Explorer allows launching of most of the TINKER programs. After selecting a routine and configuring its modifying arguments, selecting the “play” button starts the job running. If the routine completes before Force Field Explorer is exited, the textual results in the log file are loaded into the Logs panel. If Force Field Explorer exits while one or more routines are running, they continue in the background unless explicitly killed by the user.The “Optimize” command has been selected for enkephalin
8 Description of Force Field Explorer Components LogsThe Logs panel is a simple text editor where output logged from TINKER routines is automatically loaded. It can also be used to edit any text file, for example TINKER coordinate or keyword files.The Log panel shows output logged from a TINKER Optimize command on enkephalin.
9 TINKER example – AnionEstimation of the free energy of hydration of Cl- anion vs. Br- anion via a 2 picosecond simulation on a "hybrid" anion in a box of water, followed by free energy perturbationSimulated 1 anion and 214 SPC waters (Simple Point Charge water model) in a cubic Box of side Ang using minimum image periodic boundary conditions. Note the waters are kept rigid and particle mesh Ewald is used for charge interactions (see anion.key file for details)File name and extensionanion.key – keywords for the simulation, it contains values for switches and parametersanion.txt – store results for simulation, Atom Type Parametersanion.xyz – Cartesian coord. file for the anions (Cl, Br, unknown) and 214 waters
10 TINKER example – Anion anion.key file Water - angle bending parameter, K(B)=37.95, anglepartial charge of O= -0.82bond stretching parameter, K(S)=527.2
11 TINKER example – Aniondynamic anion 1000 dynamics steps, interval of the dynamics steps, interval between each coordinate saves (0.1)Next type archive anionAnswer the questions with Create, use TINKER, get the anion.arc file
12 TINKER example – AnionOpen the anion.arc file with FFE, select the ‘oscillate’ under trajectory, then click the ‘play’ button to see the movie
13 TINKER example – Anion Exercise Do the same calculation with X replaced by the chloride or bromide anionDo the calculation with the anion moves to the origin (center) of the box
14 TINKER example – Argon cp argon.1st argon.xyz Performs an initial energy minimization on a periodic box containing 150 argon atoms followed by 6 picoseconds of a molecular dynamics using a modified Beeman integration algorithm and a Bersedsen thermostat.StepsOpen the argon.xyzPotential energy programs – under the bin directory, you can copy the archive, minimize, dynamic programs to the example directoryYou may need to download the jvm.dll fileOpen the DOS console by typing cmdIn the DOS console, type in the following commands,cp argon.1st argon.xyzminimize argon 1.0dynamic argon
15 TINKER example – Argondynamic argon will generate 6 argon.xxx filesThis calculation make use of the MM3 force field parameters (under the TINKER/params directory). Full MM3(2000) parameters including pi-systems. The directional hydrogen bonding and electro-negativity bond length correction terms are implemented.Next type in ‘archive argon’Answer the questions with Create, use TINKER, get the argon.arc fileOpen the argon.arc file with FFE, select the ‘oscillate’ under trajectory, then click the ‘play’ button to see the movie
16 TINKER example - crambin Generates a TINKER file from a PDB file, followed by a single point energy computation and determination of the molecular volume and surface areaFFE ‘download from PDF’ is not functioningUse type in the PDB id icrn, save the PDB file to localOpen the DOS console, type in following commands,pdbxyz 1crn.pdb use the potential parameter file mm3pro.prm the program will convert a PDB file into a TINKER .xyz Cartesian coordinate fileanalyze 1crn.xyz epspacefill 1crn.xyz yThe analyze program - allow output of total potential energy of the system, total dipole moment, moments of inertia, radius of gyration, energies associated with specified individual interactionsThe spacefill program - compute the volume and surface areas of molecules.DSSP database -
17 TINKER example - dialanine Finds all the local minima of alanine dipeptide via a potential energy surface scan through jumping between the minimaA program for general conformational search of an entire potential energy surface via a basin hopping methodtype in ‘scan dialanine ’type in ‘archive dialanine’ Create Tinker Scan program - A program for general conformational search of an entire potential energy surface via a basin hopping method.before energy minimizationafter energy minimization
18 TINKER example - formamide Converts to a unit cell from fractional coordinates, followed by full crystal energy minimization and determination of optimal carbonyl oxygen energy parameters from a fit to lattice energy and structurecrystal formamide.cell 1 generate formamide.xyzcrystal formamide 4 y generate formamide.xyz_2newton formamide a a generate formamide.xyz_3xtalfit < formamide.dat