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.

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
3. packmol

By default, pestifer looks for these in /usr/local/bin. Specific paths for these can be stipulated in the paths directive of your input file.

Pestifer includes the July 2024 Charmm36 force field.

• 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

Cameron F. Abrams

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

https://github.com/cameronabrams

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