pestifer 1.4.1

A NAMD topology/coordinate input builder

Pestifer

Automatic NAMD System Input Builder

Pestifer is a Python utility for generating atomistic inputs with appropriate topology and parameter files required for molecular dynamics simulations using NAMD. It is intended as a fully automated system builder requiring as inputs only the PDB codes of biomolecular structures and a handful of customization parameters. Pestifer primarily works as a front end for VMD's psfgen utility.

Installation

pip install pestifer

Once installed, the user has access to the main pestifer command.

Release History

• 1.4.1:
  • support for empty TER records
• 1.4.0:
  • packmol-memgen integration
• 1.3.9:
  • added include_C_termini boolean to declash directives; set to False to prevent C-terminal insertions from undergoing automatic declashing
• 1.3.8
  • bugfix: spurious code in pestifer-vmd.tcl
• 1.3.7
  • bugfix: fixed a spurious hard-coded path in macros.tcl
• 1.3.6
  • bugfix:
    • runscript sources TcL proc files with dependencies in proc files that aren't yet sourced; fixed that
  • alphafold source directive added to permit download of models from the AlphaFold database by accession code
• 1.3.5
  • bugfix:
    • renumbering of author resids in non-protein segments if user adds protein residues by insertion that may conflict
  • transferance of atomselect macros from YAML input to any VMD script
  • inittcl subcommand makes this transfer; needs only to be run one time post-installation
• 1.3.4
  • new TcL procs for asymmetric unit generation from non-symmetric assemblies
  • pestifer_init TcL proc provided in docs for user VMD startup script
  • script subcommand removed
  • syntax of wheretcl subcommand expanded
• 1.3.3
  • NAMDLog class introduced for parsing NAMD2-generated log files
  • mdplot task for generating plots of various energy-like quantities vs timestep
• 1.3.2
  • allow for user-defined links in the config file
  • all example builds now have tests in the test suite
• 1.3.1
  • bug fixes for cleaving
• 1.3.0
  • Support for reading from already-build PSF/PDB systems
• 1.2.9
  • improved declashing and domain-swapping
• 1.2.8
  • grafts for adding glycans
• 1.2.7
  • cleave task and CleavageMod
• 1.2.6
  • ModManager replaces ModContainer
• 1.2.5
  • insertion mod; corrected bug in brot tcl procedure
• 1.2.3
  • script subcommand handles local scripts
• 1.2.2
  • added wheretcl subcommand
• 1.2.1
  • added script subcommand
• 1.2.0
  • split all namd subtasks out; now they are level-1 tasks
• 1.1.3
  • added manipulate task
• 1.1.2
  • more control over production NAMD2 config generated by the package directive
• 1.1.1
  • position restraints control in minimization and relaxation
• 1.1.0
  • other_parameters for any NAMD2 relaxation task
• 1.0.9
  • alternate coordinate files and Cfusions
• 1.0.8
  • chain-specific control over building in zero-occupancy residues at N and C termini
• 1.0.7
  • alpha crotation for folding a span of residues into an alpha helix
• 1.0.6
  • cif_residue_map_file generated to report mapping between CIF-residue numbering and author residue numbering
• 1.0.5
  • enhancements to packaging task
• 1.0.4
  • support for topogromacs added
• 1.0.1
  • Initial version

Meta

Cameron F. Abrams

Distributed under the MIT license. See LICENSE for more information.

https://github.com/cameronabrams

Contributing

1. Fork it (https://github.com/cameronabrams/pestifer/fork)
2. Create your feature branch (git checkout -b feature/fooBar)
3. Commit your changes (git commit -am 'Add some fooBar')
4. Push to the branch (git push origin feature/fooBar)
5. Create a new Pull Request