nucleosome

Development

CafeMol has been developed since 2008 at Kyoto Univeristy.

 

Contributors

The main contributor of CafeMol is Hiroo Kenzaki. The chief contributor for the earlier version of CafeMol, called CaFold, is Nobuyasu Koga. Other key contributors of CafeMol are (in alphabetical order), Le Chang, Sotaro Fuchigami, Naoto Hori, Mashiho Ito, Ryo Kanada, Suguru Kato, Hiroki Koide, Shintaroh Kubo, Wenfei Li, Toru Niina, Kei-ichi Okazaki, Kouya Sakuma, Masahiro Shimizu, Cheng Tan, Tsuyoshi Terakawa, and Xin-Qiu Yao.

The CafeMol project is directed by Shoji Takada.

 



Ver. 3.2.1 Release Notes

Changes from version 3.2 to 3.2.1

  • The handling of version numbers and command line interface have been improved.
  • The example of flexible fitting molecular dynamics simulation to an AFM image has been modified to include the protein-DNA sequence-nonspecific interactions.



Ver. 3.2 Release Notes

Changes from version 3.1 to 3.2

  • The method of compiling CafeMol has been changed to using CMake.
  • The flexible fitting molecular dynamics simulation to an AFM image is available.
  • The external potential that can be used as AFM stage is implemented.
  • A bug in the calculation using 3SPN.2C model for DNA was fixed.



Ver. 3.1 Release Notes

Changes from version 3.0 to 3.1

  • The PWMcos model for protein-DNA sequence-specific interactions are available.
  • The hydrogen-bond based model for protein-DNA sequence-nonspecific interactions are available.



Ver. 3.0 Release Notes

Changes from version 2.1 to 3.0

  • Masses and frictions of particles were changed, which led to a change in the unit of time in CafeMol.
  • New DNA models, 3SPN.2 and 3SPN.2C are available.
  • We can now use partial charges for amino acids determined by a multiscale algorithm called RESPAC.
  • The multi-canonical ensemble simulation with Wang-Landau scheme has been implemented.
  • The default charge of histidine was changed from 1.0 to 0.0.
  • The default value of the parameter “iflag_scale_aicg2” in the file “aicg_generic.para” was changed from 0 to 1.
  • Input routines for PDB files were modified to accept any orders of ATOM lines in a single DNA residue.
  • Many bugs were fixed and a number of small changes were made on top.



Ver. 2.1 Release Notes

NEW FEATURES

  • added AICG2+ interaction, which removes some faults of AICG2 interaction

BUGFIXES AND IMPROVEMENTS

  • Fixed double counting of Go interaction between protein and DNA when “i_go_atom_dna = 1”.
  • Fixed deletion of nonlocal Go interaction when using “i_del_int” option with “DEL_GO” > “DEL_BA_DIH”.
  • Fixed deletion of local Go interaction L_AICG, L_AICG2, and L_AICG2_PLUS when using “i_del_int” option.
  • Fixed local AICG2 interaction when reading from nativeinfo file with MPI parallelization.
  • Change parameter values for RNA.