---

---

Ligand-Based Drug Design Tutorial: 4. Conformational Analysis with TINKER

Introduction to Conformational Analysis

The structure that you built and optimized may or may not correspond to the lowest energy structure. In case of large molecules, the initial structure is likely to be different from the lowest energy conformer. For not too large flexible molecules, the lowest energy structure can be found by generating a large number of different conformations and minimizing each. Different conformers are generated by systematically or randomly altering the torsional angles in the molecule. Such analysis is commonly called the conformational analysis. Conformational analysis requires a large number of energy evaluations and is practical only using molecular mechanics force fields. In order to perform conformational analysis, the program should be able to recognize your molecule and assign suitable force field parameters. Because parameters for some molecular connectivities are missing, not all molecules can be analyzed with many common force fields.

Using TINKER for Conformational Analysis

We will be using a general-purpose molecular modeling software TINKER to perform conformational analysis of isopropanol. One of the reasons for using TINKER is that it is free and you can install TINKER on your personal Linux, Windows XP or MacOS computer. TINKER provides a suite of molecular-mechanics based modeling tools that can be executed from the Unix shell, linked to a third party program, such as molden, or launched from TINKER's own Java-based graphical user interface ffe. You will be running the conformational analysis calculations interactively using the Unix shell.

• Type scan on the Unix shell on the workstation. This will start one of the conformational analysis programs that comes with TINKER. The scan program searches for minima by following user-defined number of vibrational modes that correspond to torsional motions of groups.
• Give the name of the file that contains the structure of isopropanol (isopropanol.xyz).
• If a file isopropanol.key was generated during successful MOLDEN minimization, the program will ask you to confirm few run parameters. The default values are fine.
• If a file isopropanol.key is not present, the program asks for the force field file. The suitable file is at /usr/local/tinker-4.2/params/mm3.prm, then requests to confirm run settings.
• Each conformer found will be written to its own file (e.g. isopropanol.001, isopropanol.002, ....). Perform energy analysis for each conformer using TINKER's program analyze. Write down the total energy for each structure and identify the lowest energy structure. Calculate the relative energy of the higher energy structure by subtracting its energy from the energy of the lowest energy conformer.
• Examine each of the conformers found with the program MOLDEN. Type molden isopropanol.001 to analyze structure of the first conformer. Measure the HO-CH dihedral angle in each conformer. From MOLDEN, write each structure out to its own PDB file (e.g. isopropanol_cf1.pdb, isopropanol_cf2.pdb, ...) because PDB is more universal file format than TINKER's xyz.
• Close MOLDEN.

Superimposing Molecules

It is often useful to compare the three-dimensional structure of a drug candidate with the known bioactive conformer of a known ligand. One may also want to compare different conformers a molecule to see the differences between low-energy and higher energy conformers. This is often best accomplished by superimposing molecules. Molecules can be superimposed either graphically or automatically by the computer. Most commercial molecular modeling programs allow superimposing molecules. Several free programs, such as gOpenMol, PyMOL and UCFS Chimera allows users to superimpose molecules graphically. TINKER allows both automatic (via superpose program) and graphical (via the Force Field Explorer GUI) superposition of molecules. The automatic superposition in TINKER is performed using the superpose program by minimizing the RMS difference between atomic positions. You will be using UCSF Chimera in this exercise to superimpose the conformers of isopropanol.

• Start UCSF Chimera by typing chimera on the Unix Shell at the workstation.
• Open each of the conformer PDB files in Chimera.
• In Chimera, select Actions, then Color ... by element to color atoms.
• In Chimera, select Favorites, then Command Line to open the command line and molecule selector buttons.
• Overlay the heavy atoms of the two molecules so that you can observe the different geometry of the hydroxyl group in two conformers that were found. You can select which molecule to move using the radiobuttons at the bottom bar of the Chimera windows.
• You can save screen images from Chimera by selecting Save Image from the File menu.

---

---

Tutorial by Dr. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara. ©2007