Conformational Sampling (Schrodinger)

Introduction

Conformational sampling performed with Schrodinger software using default parameters.

To perform the conformational analysis the licensed Schrodinger software is required.

The licensed software is installed on the workstation, thus go to the Workstation Tips page for the instructions for the remote connections.

Workstation setup

Setup the environment variables:

It is mandatory to check if the license manager is up.

If the results is similar to this:

username 2123  1954  0 17:13 pts/1    00:00:00 grep -E --color=auto lmgrd|SCHROD

It means that the license manager is down, thus it must be started.

Then,check again the license manager status.

Now, the results should be similar to this:

username 9712  9709  9 17:34 ?        00:00:01 SCHROD -T 130.192.140.110 11.17 7 -c :/opt/schrodinger2021-1/license.txt: -srv mCPk9OT3mYyUEwshmiQCuQTcBkZfDD1cICUG2tx0YWyQSoKkXXuf2pXnaAFiJBa -daemon_port cf08 --lmgrd_start 60f83e9f -reuseaddr -vdrestart 0 -l /opt/schrodinger2021-1/lmgrd.log

If the result of the check is this after the first test, it means that the license manager is up and no operations are needed.

Load molecule(s)

Move to the working directory where the molecules are located in mol2 format using Linux cd command.

Then run Maestro

$SCHRODINGER/maestro

Select the working directory using the selection window

• Probably, the selection window is opened in the directory where you launched Maestro

File - Import structures

• Select the structure(s) to be imported
• If you import more than one structure, is better to work with distinct projects: one for each electrical state (neutral, positive charged and negative charged)

Check the structures

• In the Workspace navigator (on the right) you can select the In circle to view each structure
• For each structure assign the correct bond order
• Double click on one atom of the molecule to select all the atoms of the molecule
• Edit - Assign - Bond orders

Save the project

File - Save Project As

Conformational analylis

Run the conformational analysis

• Click on the Tasks button at the top right
• Digit Conformational search in the window
• Select Conformational Search Macromodel
• Select the molecules in the ENTRY LIST
• The names have to be highlighted in cyan
• Change three parameters
• In the Use structures from selection menu, choose Project Table (selected entries)
• Select the solvent in the drop down menu
• Change the job name in the bottom with a name related to the simulation
• In particular, mention explicitly the solvent
• Click Run bottom
• Now you can close the setup window
• Using the button Jobs it is possible to follow the job
• Finally, jobs work in background thus it is possible to close projects and exit from Maestro
• Loading the project, the results will be added at the end of the job

Analysis of the results

Run Maestro if it is necessary following the procedure shown in Load molecule(s)

• File - Open Project
• Select the project
• If the job is finished the results are automatically incorporated in the Workplace Navigator
• Select the conformations of a single molecule in the Workplace Navigator (highlighted in blue after selection)
• Click on the right button of the mouse and select Export - Structures
• Check that Structure source to be exported option is set to Project Table (selected entries)
• Digit a File name with the extension mol2
• The structures are saved in a multimol2 file
• Use a name that helps to remember the type of simulation performed, in particular the used solvent and ionization state
• In Maestro select Windows - Project Table
• The spreadsheet with Energy values is shown
• If necessary select the entries correspondent to the conformations previously exported in mol2 format (highlighted in blue after selection)
• In the Project Table window click on Data - Export - Spreadsheet
• In the Export window set:
• Entries: selected
• Properties: selected and use the select options to select conformation options, Entry ID, Entry Name, Potential Energy, Relative Potential Energy, Serial Number
• Delimiter: comma
• File name: the same name of mol2 file with extension csv

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