Facio 14. 3. 2003 download by Masahiko Suenaga
Facio is an OpenGL-based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations (GAMESS and Gaussian).
SSH / SFTP client is also implemented. Through SSH / SFTP connection, Gaussian job can be submitted to batch job system on the remote server and calculation results can be retrieved form the server. Supported batch job systems are LoadLeveler and NQS.
Since Facio internally uses PDB (Protein Data Bank) format, it can also display a 3D-structure of biological macromolecules, such as proteins and nucleic acid with emphasizing their secondary or quaternary structures.
1. Molecular Modeling Features
Modeling is simple. Replacing a hydrogen with CH3, CH2, CH, Phenyl, OH, Formyl, NH2 and Glycosyl, molecular model is assembled. Besides ordinary functions required for molecular modeling, Facio featues the following functions.
Geometry Optimization with PC GAMESS or WinGamess
Rendezvous and Docking of Two Molecules
Two molecular files (in PDB format) can be successively loaded.
And the relative position of the latter molecule can be adjusted.
Any two bonds of each two molecule can be aligned.
Two hydrogen atoms are deleted.
Making a bond.
Group can be moved along the bond.
With Facio, you can make a model of a large and complex molecule, such as Ciguatoxin, a marine natural product.Ciguatoxin
2. Visualization of Quantum Chemical Calculations
Facio can visualize CUBE Molecular Orbital data of PC GAMESS and Gaussian.
Facio reads GAMESS punch file or Gaussian output file for normal mode of vibration to display it as an animation ,which is more animated than those shown here.
3. Viewing Biological Macromolecule
Facio's native molecular structure format is PDB (Protein Data Bank). Thus, protein or nucleic acid data in PDB format is loadable to Facio. In the former version, Facio sometimes collapsed with fatal exception. This fatal bug has been fixed for the latest version. However, there still exist PDB files that Facio cannot parse.
Tags: analyze molecule , Modeling , Molecular Modeling , quantum chemical calculation visualization , Visualization , Visualize