A NAMD topology/coordinate input builder
Project description
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
- 1.3.5
- 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
- bugfix:
- 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 scriptscript
subcommand removed- syntax of
wheretcl
subcommand expanded
- 1.3.3
NAMDLog
class introduced for parsing NAMD2-generated log filesmdplot
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 andCleavageMod
- 1.2.6
ModManager
replacesModContainer
- 1.2.5
insertion
mod; corrected bug inbrot
tcl procedure
- 1.2.3
- script subcommand handles local scripts
- 1.2.2
- added
wheretcl
subcommand
- added
- 1.2.1
- added
script
subcommand
- added
- 1.2.0
- split all namd subtasks out; now they are level-1 tasks
- 1.1.3
- added
manipulate
task
- added
- 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
- Fork it (https://github.com/cameronabrams/pestifer/fork)
- Create your feature branch (
git checkout -b feature/fooBar
) - Commit your changes (
git commit -am 'Add some fooBar'
) - Push to the branch (
git push origin feature/fooBar
) - Create a new Pull Request
Project details
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