pestifer

Pestifer

Automatic NAMD System Input Builder

Pestifer is a fully automated system builder, requiring as inputs only biomolecular structures (e.g., PDB IDs, PDB files, mmCIF files, alphafold IDs) and a handful of customization parameters, to generate NAMD-compatible input files (PSF, PDB). It is basically a front end for VMD's psfgen utility. It also has a few handy subcommands for working with NAMD output.

Installation

pip install pestifer

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

Pestifer also requires access to the following executables:

1. namd2 and charmrun
2. vmd and catdcd
3. packmol

By default, pestifer looks for these commands in your path. Specific paths for these can be stipulated in the paths directive of your input file.

Pestifer includes the July 2024 Charmm36 force field.

Documentation

Please visit readthedocs for full documentation.

Release History

• 1.7.2
  • bugfix:
    • correct the detection of whether or not a file is a NAMD log file based on the first two Info: records
    • correct the problem with restarts interfering with mdplot
• 1.7.1
  • make-namd-restart enhanced with SLURM script updating
• 1.6.4a2
  • bugfix: GPU-resident NAMD3 cannot do mulitple-gpu runs with constraints
• 1.6.4a0
  • all lipids in the charmmff topology file top_all36_lipid.rtf now have PDBs ready for packmol
  • show-resources subcommand enabled
  • make-namd-restart subcommand enabled
  • ycleptic dependency updated to 1.1.0
• 1.6.1
  • now able to use namd2 or namd3
  • can optionally use GPU-resident namd3
• 1.5.9
  • bugfix: log write suppressed inadvertently if progress bars not used
• 1.5.6
  • desolvate subcommand implemented
• 1.5.5
  • wildcard allowed in pdbalias commands for atom renaming
  • temporary fix for dbRes HIS in any mutations to be named HSD
• 1.5.4
  • bugfix: incorrect deletion of image seqmods
• 1.5.3
  • bugfix: custom_pdb_path bug in bilayer fixed
• 1.5.2
  • glycan graph mistake fixed
  • python dependency updated to >=3.12
  • ycleptic dependency updated to 1.0.7
• 1.4.8
  • updated CHARMM lipid PDB files
  • updated ycleptic to 1.0.6 to enable interactive help and automatic config documentation
• 1.4.7
  • ambertools dependency removed
  • packmol-memgen integration removed; now use native bilayer task
  • make-resi-database command added
  • CHARMM force field files updated to July 2024
  • salt_con, anion, and cation specs for solvate now available
  • pidibble dependency updated to 1.1.9
• 1.4.6:
  • pierced ring detection and remediation via the ring_check task
  • restart task added
  • automatic detection of SLURM environment for multi-node MD runs
  • --config-updates option for fetch-example and run-example subcommands implemented
  • progress bars enabled for NAMD, psfgen, and packmol
  • --kick-ass-banner option implemented -- check it out!
  • pidibble dependency updated to 1.1.8
  • expanded integration of packmol-memgen
• 1.4.5:
  • added fetch-example subcommand that just copies the respective example YAML file to the CWD
  • bugfixes:
    • since packmol-memgen sometimes translates the insert, cannot use packmol's input coordinates to psfgen the resulting embedded system
• 1.4.4:
  • now includes Tcllib 2.0
  • bugfixes:
    • fixed incorrect charges on the C-terminal CA and HB in the HEAL patch
• 1.4.3:
  • update ambertools version requirement to 23.6; no more packmol-memgen/pdbremix error
  • bugfixes:
    • change packmol-memgen's weird ion names to be CHARMM-compatible
    • allow for N-atom position calculation for residues added to a C-terminus (atom name OT1 vs O)
• 1.4.2:
  • explicit chain mapping in config file
• 1.4.1:
  • support for empty TER records
• 1.4.0:
  • initial 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 release

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