Tinker User's Guide

TINKER

Tools for Molecular Design

Version 8.10 February 2023

Copyright ? 1990-2023 by Jay William Ponder All Rights Reserved

User's Guide Cover Illustration by Jay Nelson Courtesy of Prof. R. T. Paine, Univ. of New Mexico

TINKER IS PROVIDED "AS IS" AND WITHOUT ANY WARRANTY EXPRESS OR IMPLIED. THE USER ASSUMES ALL RISKS OF USING THIS SOFTWARE. THERE IS NO CLAIM OF THE MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

YOU MAY MAKE COPIES OF TINKER FOR YOUR OWN PERSONAL, ACADEMIC OR NONPROFIT USE, AND YOU MAY MODIFY THOSE COPIES. YOU MAY NOT DISTRIBUTE ANY ORIGINAL OR MODIFIED SOURCE CODE, EXECUTABLES OR DOCUMENTATION TO USERS AT ANY SITE OTHER THAN YOUR OWN.

PLEASE READ THE FULL TINKER LICENSE, AND SIGN AND RETURN THE LICENSE AGREEMENT IF YOU MAKE USE OF THIS SOFTWARE. COMMERCIAL USE OF TINKER IS GOVERNED UNDER A SEPARATE AGREEMENT AS DESCRIBED IN THE FULL TINKER LICENSE.

V8.10 02/23

Tinker User's Guide

TinkerTools Organization

Feb 20, 2023

CONTENTS

1 Introduction to the Software

1

1.1 What is Tinker? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.2 Features and Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.3 Contact Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2 Installation on Your Computer

5

2.1 How to Obtain a Copy of Tinker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.2 Prebuilt Tinker Executables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.3 Building your Own Executables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.4 Tinker-FFE (Force Field Explorer) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2.5 Documentation and Other Information . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2.6 Where to Direct Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3 Types of Input & Output Files

9

4 Potential Energy Programs

13

5 Analysis & Utility Programs & Scripts

21

6 Force Field Parameter Sets

27

7 Special Features & Methods

35

7.1 File Version Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

7.2 Command Line Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

7.3 Use on Windows Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

7.4 Use on MacOS Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

7.5 Atom Types vs. Atom Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

7.6 Calculations on Partial Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

7.7 Metal Complexes and Hypervalent Species . . . . . . . . . . . . . . . . . . . . . . . 38

7.8 Neighbor Methods for Nonbonded Terms . . . . . . . . . . . . . . . . . . . . . . . . 39

7.9 Periodic Boundary Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

7.10 Distance Cutoffs for Energy Functions . . . . . . . . . . . . . . . . . . . . . . . . . . 39

7.11 Ewald Summations Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

7.12 Continuum Solvation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

7.13 Polarizable Multipole Electrostatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

7.14 Potential Energy Smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

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