Optional Parameters

Basic options

-out <filename>

Molecular output file name in any format supported by OEChem. The default name is freeform.oeb. For free energy estimation of the conformations for the input molecule, the output file contains all unique solution conformations structures identified by freeform. In the case of solvation free energy estimation, the output file contains the lowest energy vacuum conformation for which the PB solvation calculation was actually done.

-param <filename>

Command line options will be read from the specified file. This file may have been generated from a previous run or may be constructed de novo. The default name of the file is freeform.param. Any parameter in the parameter setup file is superseded by the parameter on the command line.

-prefix <p>

Replaces freeform prefix in .log, .param, .oeb and .pdf output files, with the input string p.

-report <filename>

Name of the graphical output file. Currently only pdf and ps formats are allowed. The default name is freeform.pdf.

-track <filename>

The molecular input of conformers to be tracked is read from the file name; any 3D molecule file format supported by OpenEye is acceptable. Of critical importance is that the molecule graph be identical to that specified in the -in input file, and that atom and bond ordering also be identical. For the most common uses of freeform, the same input file is specified for both the -in and -track options.

Advanced options

-ensemble

The ensemble of conformations is read from the -in input file instead of being generated internally. In both cases of -calc option, this ensemble is treated as if it already contains all the conformations needed. In conformer free energy estimation, when used together with -track, the tracked conformations are included with the ensemble.

-ewindow

The -ewindow flag sets the energy window (in kcal/mol) used as an energy cutoff in the initial conformation generation stage of freeform. An ewindow of at least 15.0 is encouraged to better cover accessible conformational space; increasing ewindow will increase the number of conformers. [default = 15.0]

-ff <type>

This option specifies which forcefield to use in the energy minimizations and thermodynamics calculations following the initial conformer search. By default MMFF94S is used; this can be specified explicitly by setting parameter type to mmff94s). Alternatively, setting parameter type to mmff94 means the MMFF94 forcefield will be used instead. The two differ in how conjugated trivalent nitrogens are treated: with MMFF94S they tend to be more planar whereas with MMFF94 they tend to be more pyramidal.

-ionic <type>

By default a charge state used in calculations corresponds to pH = 7.4 (the value of parameter type is set at pH74). Two remaining values are uncharged and input. The former corresponds to an uncharged ionic state (i.e. no formal charges); the latter to the preexisting ionic state determined from the molecule input file.

-maxconfs <value>

The -maxconfs flag sets the maximum number of conformations to be generated using OMEGA for the initial conformation generation stage of freeform. A large set is desirable to cover the conformational space necessary to include all reasonable conformers that might contribute to the partition function. When this initial set is minimized a large reduction is expected in the number of unique minima. [default = 40000]

-rms <value>

RMS threshold for conformations generations with OMEGA. The default value is calculationDependent meaning that the RMS threshold used depends on whether “-calc conf” or “-calc solv” is being run. 0.3 Å is used with “-calc conf” and 0.6 Å with “-calc solv”. Values ranging from 0 to 5 are accepted.

-solvent <type>

By default Sheffield solvation is used with dielectric 80.0 to account for aqueous solvation of the unbound ensemble; this can be specifically requested by setting the parameter type to sheffield. Setting type to PB will result in Poisson-Boltzmann (PB) single-point solvation energies being calculated at the Sheffield-based minima. The default solvent dielectric for the PB calculation is 80.0, but this can be changed with the -PBsolvent_dielectric option. Setting type to vacuum means that no solvation energy will be calculated.

-PBsolvent_dielectric <value>

This option allows the user to change the solvent dielectric used in the PB single-point solvation energies requested with -solvent PB. The default value is 80.0 to approximate aqueous solvation; it can adopt any value between 1.0 and 80.0 .

-solvcharges <type>

Selects the type of partial charges to be used for the solvent forces. By default the value of type is calculationDependent meaning that the charge type used depends on whether “-calc conf” or “-calc solv” is being run. AM1BCC charges that are AM1-optimized (Opt) (constrained to starting geometry) and symmetric by 2D-bond symmetry (Sym) are used for conformer free energy estimation and non-symmetric (NoSym) AM1-single-point (SPt) for solvation free energy calculations. For net-charged species however, mmff94 charges are used for the conformer free energy estimation, even if the flag value selected is different than mmff94. The defaults are different because the science behind the solvation free energy calculation ([Nicholls-2010]) was specifically developed using the “NoSymSPt” variant of AM1BCC charges whereas the conformer free energies require the robustness of the canonical AM1BCC charging scheme (symmetric charges from a constrained AM1 optimization) towards large changes in conformation over the course of geometry optimization. In addition to the default calculationDependent, the other possible values of the parameter type are: am1bccSymOpt, am1bccNoSymOpt, am1bccSymSPt, am1bccNoSymSPt, mmff94 and input. The first four refer to different variants of the AM1BCC charging scheme; the next applies MMFF94 charges and the last is used to specify user-defined charges (which are read in from the input structure). If input is selected then the value of “-ionic” is automatically set to input.