ParamIT: a Toolset for Molecular Mechanical Force Field Parameterization within the CHARMM/CGenFF Protocol
December 24, 2013: Good news, we are back to active development of ParamIT. We are currently working on following features:
- Support of GAMESS-US and NWChem for quantum chemical calculations
- Manual force constants optimizations without CHARMM the programm
- Automatic force constants optimization
- Dihedral terms optimization without CHARMM the programm
Estimated delivery time: summer 2014. If you would like to participate in beta-testing please send us e-mail.
November 9, 2012: Finally, we are making first public release, which got version number 1.0. See Download for files. BSD license was chosen for ParamIT. ParamIT can work only on Linux x86-64 platforms.
November 2, 2012: almost there, the first release coming very soon, if you want to get informed send an e-mail to firstname.lastname@example.org with title "Inform me about ParamIT release"
Briefly About ParamIT
ParamIT is a toolkit aiding the development of molecular mechanical force fields within the CHARMM/CGenFF protocol for small, drug-like, molecules. Given the massive variety of organic compounds, quite often the parameters for small organic molecule of interest are not present in existing molecular force fields thus are needed to be developed. To aid the parameterization ParamIT features several graphical plug-in to VMD and automatic fitters for charge and dihedral terms optimizations. To facilitate the automatic fitting procedures several computationally demanding routines were implemented in C with OpenMP parallelization.
While we are working on bringing more information, some preliminary overviews can be seen at:
Some technical details:
- License: BSD
- Platform: Linux x86-64
- Programming languages: C and Python
- Distribution: binaries with source code
- VMD is needed for some programs
Requirements for ParamIT (binary distribution)
ParamIT is mainly written in python with some functionality implemented in C (for speed benefits). ParamIT includes command line utilities and graphical plug-ins to VMD. ParamIT is distributed in binary form for with all sources. Because only Linux's VMD support python almost out of the box (proper version of the python needed) we provide binaries only for Linux x86-64. Because binary VMD linux distribution compiled against out-dated python, rarely seen any longer on modern Linux desktops, ParamITPack also has proper python distribution compatible with VMD.
Here is what you need in order to use ParamIT to full extend:
- Platform: Linux x86-64
- VMD Version 1.9.1 (2012-02-04) LINUX_64 OpenGL, CUDA
- Gaussian 09 for all QC calculations
- For parameters optimization, ParamIT uses xyz files with other important information written in xyz file header line. Therefore the user can create such xyz-file by hands.
- CHARMM version higher then c36b1, if other versions is used CGenFF patch should be applied.
- CHARMM, the program, used for dihedral scans and vibrational analysis. Charge optimization does not use CHARMM the program.
Current Stage as of October 4th, 2012
Unfortunately the progress in the developments of ParamIT has been getting slow recently due to the developers relocation. The ParamIT was developed in Pittsburgh Supercomputing Center (National Resource for Biomedical Supercomputing) by Nikolay Simakov and Troy Wymore. Both authors are currently in the relocating and establishing process at new places. But be patient we are working on the first release and documentation.