Conformational sampling (freeform)

Setup of the environment

Windows

Run the "OpenEye-Applications Ver" command line.

The Command Prompt window opens.

Move to the working directory where the mol2 input files are located.

In the Command Prompt digit the following commands.

cd c:\Users\username\directory

where the directory Users is the default directory for user sub-directories and username is the sub-directory of the user. It is possible to use the file manager to find the full name of the directory.

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

Move to the working directory where the mol2 input files are located.

In the bash windows digit the following commands.

cd namedirectory/namesubdirectory

Pay attention to the slash that is different for Linux and Windows.

Conformational sampling with freeform

To run the freeform experiment in chloroform:

freeform -calc conf -in mol.mol2 -report mol_chl.pdf  -prefix mol_chl_free -solvent PB -PBsolvent_dielectric 4.81 -out mol_chl.mol2 -ionic input

To run the freeform experiment in water:

freeform -calc conf -in mol.mol2 -report mol_wat.pdf  -prefix mol_wat_free -solvent PB -PBsolvent_dielectric 80.0 -out mol_wat.mol2 -ionic input

Ionic flag is set to input to maintain the original ionic state.

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