pestifer 1.20.2

A NAMD topology/coordinate input builder

Pestifer

NAMD System Preparation Tool

Pestifer is a fully automated simulation-ready MD system preparation tool, 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, and xsc). It is basically a highly functionalized 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

• 1.20.2
  • upgraded example support
• 1.19.1
  • fixed namd restart bugs
• 1.19.0
  • fixed improper sorting of segment indices in bilayer_embed.tcl
  • support for adding, renaming, inserting, assigning authorship to, and deleting examples
• 1.18.1
  • switched from patches to mutations for protonated histines predicted by pdb2pqr
• 1.18.0
  • developer support for adding examples
• 1.17.0
  • support for simple nucleic acids added
• 1.16.3
  • fixed None-return bug in terminate task
  • fixed bug in insulin example to correctly assign NE2-Zn bonds
  • fixed bug causing piericing of PRO807 in model-building missing residues in insulin receptor example
• 1.16.0
  • new pdb2pqr task to assign protonation states based on propka3
• 1.15.1
  • fixed the dropped filename extensions in mdplot
• 1.15.0
  • updated salt concentration implementation in membrane system builder
  • removed spurious dependence on parmed
  • added pressure profile calculation capabilities to mdplot task
• 1.14.1
  • new docs
• 1.14.0
  • Implemented standard CHARMM36 patches as mods
  • Added HIV-1 protease 1f7a as a new example (now there are 16!)
• 1.13.3
  • Allow config to contain names of otherwise unnamed lipids in CHARMMFF
• 1.13.2
  • Example 15 added with ring-check
• 1.13.1
  • changed make-resi-database to make-pdb-collection
  • updated PDB repository to work with a gzipped folder (all lipids)
• 1.13.0
  • converted charmmff contents back into an as-downloaded tarball
• 1.12.1
  • added half_mid_zgap parameter to ease membrane packing
  • added C6DH and C7DH lipid residue aliases for C6DHPC and C7DHCP, respectively
  • enable inadvertantly unimplemented user selection of number of lipids per leaflet in a patch
  • misspelled "paramfiles" in ycleptic basefile (one time)
• 1.12.0
  • documentation upgrades
  • better progress bar integration with packmol
• 1.11.3
  • fixed residue misnumbering for large membranes
  • fixed large membrane embedding errors
• 1.11.2
  • fixed parsing error converting specstrings to composition dicts
• 1.11.1
  • tests passed after minor updates
• 1.11.0
  • New bilayer build protocol
  • New NAMD and packmol on-the-fly log parsing, including in standalone mode with the follow-namd-log subcommand
• 1.10.0
  • Updated the pestifer_init TcL script definition to allow the command pestifer_init to replace the clunkier source [pestifer_init]
  • cleanup subcommand added for cleaning up after an aborted run
• 1.9.0
  • transrot mod enabled for global translations and rotations
  • desolvate subcommand now can output a single pdb file
• 1.8.3
  • fixed bug for growing alpha helices in the N-terminal direction in crot.tcl
• 1.8.2
  • fixed failure to avoid deprecated namd parameters if using namd2
  • fixed hard-coded C-direction brot call to detect whether brot is N- or C-terminal
  • added --gpu option for the run and run-example subcommands
• 1.8.1
  • removal of tcllib from resources (I never used it anyway)
  • bugfix in slow build tests
• 1.8.0
  • new source code structure
  • mmCIF convention updated
  • mdplot subcommand added
• 1.7.4
  • bugfix:
    • xst trace for mdplot fails if empty
• 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 automatic 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-built 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

https://github.com/cameronabrams

Pestifer is maintained by Cameron F. Abrams

Pestifer is distributed under the MIT license. See LICENSE for more information.

Pestifer was developed with support from the National Institutes of Health via grants GM100472, AI154071, and AI178833.

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