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Tutorial

Tutorial. Moshe Goldstein Fritz Haber Research Center, Hebrew U. February 13, 2012. Tutorial Plan. What is TINKER ? Basic Principles of TINKER Operation What can be done with TINKER ? mgTINKER - my version of TINKER What can be done with mgTINKER ?

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Tutorial

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  1. Tutorial Moshe Goldstein Fritz Haber Research Center, Hebrew U. February 13, 2012

  2. Tutorial Plan • What is TINKER? • Basic Principles of TINKEROperation • Whatcan be done with TINKER? • mgTINKER - my version of TINKER • Whatcan be done with mgTINKER? • Whatcannot be done with TINKER/mgTINKER? • Usingother packages for/withTINKER • Some practice with TINKER and mgTINKER

  3. What is TINKER? TINKER is a Molecular Mechanics package developed at Prof. Jay W. Ponder’s Lab, in the Department of Chemistry at Washington University, in Saint Louis, Missouri, USA.

  4. What is TINKER? • TINKER is a set of relatively independent programs written in Fortran. • Until version 5, it was written in (sequential) Fortran 77. • The latest version 6, written in Fortran 95, supports OpenMP parallelism.

  5. Basic Principles of OperationMolecule Representation SEQ filethatincludes theamino acidssequence of a peptide or protein XYZ Cartesian Coordinates fileincludes connectivityand force field-related data PRM fileincludes force fieldparameterizationdata INT Internal Coordinates fileincludes Z-Matrixand force field-related data

  6. Basic Principles of OperationCartesian Coordinates Representation

  7. Basic Principles of OperationInternal Coordinates Representation

  8. Basic Principles of OperationPeptide Sequence Files

  9. Basic Principles of Operation Affecting Calculationswith aKey Files

  10. Basic Principles of OperationAllowing Continuation ofMDwith DYN Files

  11. molecule PROGRAM molecule Calculated value(s) molecule(s) PROGRAM molecule(s) PROGRAM molecule(s) File and/or cmd params Translator/ Constructor File Basic Principles of OperationKindsofPrograms Output Input

  12. Whatcan be donewith TINKER?

  13. Whatcan be donewith TINKER?

  14. mgTINKERmy version of TINKER • mgTINKER is a system of relatively independent Python scripts that integrate together one or more TINKER programs. • TINKER programs are used as basic “black” boxes, as basic components in order to accomplish more complex computational tasks. • The code of several TINKER programs has been changed, and/or combined in order to execute new innovating operators/functions.

  15. mgTINKERmy version of TINKER Tinker 3.9 Tinker 4.0 Writtenin Fortran77 Tinker 4.1 mgTinker Mostly Writtenin Python Tinker 5.1 Writtenin Fortran95 + OpenMP Tinker 6.0

  16. Whatcan be donewith mgTINKER? • DEEPSAM, an evolutionary protein structure prediction algorithm that integrates together the advantages of the Diffusion Equation Method, Simulated Annealing, L-BFGS and Evolutionary Programming. It was written in Python, and uses existing TINKER programs and also re-written/adapted versions of them.

  17. Whatcan be donewith mgTINKER? • Several utilities has been written in order to calculate energies and superposition of series of structures calculated by DEEPSAM, and also by minimizations and simulations like MD, MC, SA, DEM, etc.

  18. Whatcannot be donewith TINKER/mgTINKER? • One of the most important disadvantages of TINKER is that it does not support non-standard (engineered) amino acids. • It is possible to add such a capability, but it requires (a) a lot work in development of additional force field parameters, and (b) a lot of programming work – the Fortran code needs to be expanded to deal with this.

  19. Whatcannot be donewith TINKER/mgTINKER? • TINKER supports calculations with implicit solvent models like GBSA, with explicit solvent boxes, in the gas phase, etc., it supports calculations on clusters of water and other kinds of molecules, but it does not support Docking calculations. • I am not sure if TINKER supports calculations on complexes of different bio-molecules. I need to check this point.

  20. Usingother packages for/withTINKER • There exists an API between GAMESS and TINKER that allows QMMM calculations (I have not tried it yet). TINKER programs work as Molecular Mechanics subroutines of GAMESS. • There exists a program called Packmol that allows to build an explicit solvent box and put a bio-molecule inside it, generating an file processable by TINKER. • …

  21. SomePracticewith TINKER and mgTINKER

  22. Tutorial THE END Moshe Goldstein Fritz Haber Research Center, Hebrew U. February 13, 2012

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