Number of IMHBs (Chimera)

Introduction

IMHBs are found on the basis of atom types and geometrical criteria.

Possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair. H-bonds involving other types of atoms are not considered.

The geometric criteria are based on a survey of small-molecule crystal structures, as described in Mills, J.E.J.; Dean P.M. Journal of Computer-Aided Molecular Design, 10 (1996) 607-622.

Data input

Conformers must be formatted as multi-pdb files.

Generally, the output of the conformational sampling is in multi-mol2 format, thus it must be converted.

Conversion of multi-mol2 to multi-pdb

It is possible to use directly Vega

Launch Vega

• Open the multimol2 file File - Open - click on the multimol2 file
• File - Save trajectory - select pdb format

Launch OpenBabelGUI

• Select mol2 as the input format
• Click on the file selection window to select the mol2 file
• Select pdb format as output format
• In the text field Output file digit the name of the converted file
• Use the same name of the input file changing the extension (from mol2 to pdb)
• Click on CONVERT button
• The new file should be created in the same directory

Input of the conformers in Chimera

Launch Chimera

• Tools - MD/Ensemble Analysis - MD Movie
• Select PDB as Trajectory Format
• Select PDB frames contained in single file option
• Use the Browse to navigate to the working directory, click on the name on the working pdb file and click on Set Input location
• Click on the ok button
• The conformers are loaded as a trajectory and are visible in Chimera
• It is possible to navigate through the conformations using the commands in the tool

Determination of IMHBs

• Tools - Utilities - Reply Log
• A Reply Log windows is shown
• Click on the Clear bottom to clear all the text in the Reply Log
• In the MD Movie panel click on the Per-Frame label and then Define script
• A windows named Per-Frames Commands appears
• In the Per-Frames Commands windows digit:

• Click the Apply bottom
• This step is important to find IMHBs for all conformers because the next step starts to register IMHBs from the second conformer
• In the MD Movie windows
• deselect the Loop option
• click on the > bottom to launch the calculation on the whole conformer ensemble
• When the calculation was performed on the whole ensemble save the Reply Log content clicking on Save bottom in the Reply Log window

Finally, click on the Quit bottom in the MD Movie panel to exit