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Description

profilerTools is a suite of Python programs to perform molecular torsional scans and parameterize the related torsional and nonbonded parameters. It is based on (classical) molecular mechanics.

profilerTools is composed of two scripts:

  • profilerGen, for obtaining torsional-scan trajectories and their energy profiles;

  • profilerOpt, for the parameterization of torsional terms and the related 1,4 Lennard-Jones terms;

For implementation details, usage instructions and a tutorial, please consult the documentation.

Installation

Recommended Installation

The recommended installation requires the numpy C header files and the GNU Scientific Library (GSL) header files. Therefore, you will face issues if you do not have GSL installed or if your numpy installation does not include the header files. For the APT package manager, this can be remedied with

sudo apt install python-numpy libgsl-dev

For other package managers (e.g., YUM and RPM), the GSL may be available under the name gsl-devel. Alternatively, you can install these libraries from their official repositories.

Once these requirements are taken care of, you can install profilerTools with the command

python setup.py build install

After that, the two executables profilerOpt and profilerGen should be available as commands in your PATH.

Note that, depending on your default installation path, you may need to run this command with administrative privileges.

Suboptimal Installation

If you have any problems obtaining the numpy and/or GSL header files, you can install profilerTools without relying on them with the command

python setup.py build install --without-geometrypy --without-gsl

After that, the two executables profilerOpt and profilerGen should be available as commands in your PATH.

Note that, depending on your default installation path, you may need to run this command with administrative privileges.

The consequences of this installation when compared with the recommended one are:

  • a worse performance of the molecular-mechanics calculations
  • no support for regularized regression in the optimization

Requirements

  • python (>=3.6)
  • numpy (automatically installed by setuptools)
  • DEAP (automatically installed by setuptools)
  • scikit-learn (automatically installed by setuptools)
  • GNU Scientific Library (optional, must be manually installed)
  • the numpy header files (optional, must be manually installed)

Limitations

  • The program is designed for small systems, and, for this reason, all nonbonded interactions are calculated explicitly (i.e., no cutoff truncation).

  • The current implementation of molecular-mechanics calculations is not optimal in terms of speed (even without taking the previous item into account).

Utilities

To facilitate the use of profilerTools, we provide additional programs to convert topologies from other formats to the .stp format. They are

  • gromacs_itp_to_stp, to convert from GROMACS .itp files;

  • gromos_top_to_stp, to convert from GROMOS .top files;

These programs, each in a separate directory, can be found in the directory utils. For usage instructions, please consult their README files.