Conformational sampling (Szybki/Omega)

Setup of the environment

Windows

Run the "OpenEye-Applications Ver" command line

Linux

The setup depends on the workstation but, in general, the license file, the required libraries and the binary executable should be found by the software.

export LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
export PATH=/opt/openeye/bin:$PATH
export OE_LICENSE=/opt/openeye/oe_license.txt

Many jobs take a long time, so it is advisable to run the job in background and close the MobaXterm session.

To do this you need to use nohup and & commands following the general syntax:

nohup COMMAND &

e.g.:

nohup oeomega classic -commentEnergy true -ewindow 10 -maxconfs 1000000 -strict -in mol_sz.mol2 -out mol_oel.mol2 -prefix mol_oel -mpi_np 4 &

WARNING: background jobs ONLY works if you exit the MobaXterm session using CRTL d keys sequence. If you exit by clicking on the cross at the top right of the MobaXterm window or using OTHER METHODS, the JOB STOPS.

First minimization with Szybki

The goal of this step is the setup of a correct and minimized structure that will be the starting point of the next steps. It is important that this structure is careful checked from a chemical point of view and that the file is formally correct. Check bond order, charges, names and all it was discussed before.

Minimization of the mol2 file with default parameters, now the dielectric setup is not important yet.

In the "OpenEye-Applications Ver" command line, run Szybki

szybki -mpi_np 8 -in mol.mol2 -out mol_sz.mol2 -prefix mol_sz

Generation of conformations

The file prepared in the step above is submitted to Omega for the conformational sampling.

The most recent versions of Omega does not implement a search dependent on the environment, thus the dielectric constants will be taken into account in the next steps.

oeomega classic -commentEnergy true -ewindow 10 -maxconfs 1000000 -strict -in mol_sz.mol2 -out mol_oel.mol2 -prefix mol_oel -mpi_np 4

For cyclic compounds

oeomega macrocycle -commentEnergy true -ewindow 10 -maxconfs 1000000 -strict -in mol_sz.mol2 -out mol_oel.mol2 -prefix mol_oel -mpi_np 4

Then the conformations are definitively minimized submitting the Omega the output to Szybki. This software also calculates and writes the final energy of the conformers.

Final minimization with Szbyki

The command to run a minimization in chloroform is:

szybki -mpi_np 4 -solv_dielectric 4.81 -current_charges true -ff mmff94s -solventPB -solventCA 0.005 -prefix mol_sz_chl -in mol_oel.mol2 -out mol_sz_chl.mol2 -report

The command to run a minimization in water is:

szybki -mpi_np 4 -solv_dielectric 80.0 -current_charges true -ff mmff94s -solventPB -solventCA 0.005 -prefix mol_sz_chl -in mol_oel.mol2 -out mol_sz_chl.mol2 -report

Szybki writes the final energy of the conformations in a report (extension .rpt) that will be used for the final report.

The dielectric constant should be set on the basis of the explored environment. Some useful values are the following:

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