Fixed bug when giving secondary structure as string. Fixed bug involving BBBB dihedrals in extended regions. Fixed bug with counter in multi chain topologies. Added function to handle new polar and charged residues in Martini 2.2P Forcefield now available: Martini 2.1, Martini 2.1P, Martini 2.2, Martini 2.2P, Elnedyn, Elnedyn 2.2 and Elnedyn 2.2P Major clean-up and restructuring of the code Bug fix: assignment of secondary structure Bug fix: bond length in Martini 2.2 & 2.2p Martinize.py (version 2.1, August 23 2012) Cleaned up and added help text and warning messages. Fixed small inconsistencies in elnedyn forcefields. Bug fix: bead types correctly set in helix starting at first residue. Added charged His to all forcefields and options to choose the His-charge state. Martinize.py (version 2.2, November 27 2012) Bug fix: Correctly merge topologies of multiple change in case of Martini 2.2P Bug fix: Correct error message when atoms are missing. Martinize.py (version 2.3, February 13 2013) Bug fix: Position restraints are correctly written out when multiple chains are merged. Bug fix: Cys-bond length and force constant Changed protein backbone constraints to bonds Inverted "define NO_RUBBER_BANDS" behavior. Martinize.py (version 2.4, August 18 2013)
Bug fix: Fixed cases where Cys-Cys constraints were not recognized as such Removed warnings about beta status of Martini 2.2. Martinize.py (version 2.5, August 11 2015)
Many, many code clean-ups and restructuring. Cys bonds in gro-files and pdb-files without chain identifier are now correctly identified. The option for the elastic bond lower cutoff (-el) is now correctly recognized. Martinize.py and python 3 version martinize.py (version 2.6, May 12 2016) The major updates are always added also here below: You can now also download the latest martinize from GitHub. If you would like to use this, send us an e-mail. If you want to make changes yourself or add a forcefield we have a modular version available. Any feedback is more than welcome! The script is "concatenated": all the different classes, modules and forcefields are in one file. The current version (2.x) has been used rather extensively, however it might still contain errors or bugs. The produced topology and structure files are in a format suitable for Gromacs. It replaces the old seq2itp, atom2cg and ElNeDyn scripts. Martinize is a python script to generate Martini protein topology and structure files based on an atomistic structure file. Last Updated: Thursday, 17 August 2017 11:59
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