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pestifer 2.5.2 documentation

pestifer 2.5.2 documentation

Introduction
Installation
Usage
- config-help
- build
  - fetch
  - continuation
  - merge
  - psfgen
    - patches
    - mutations
    - deletions
    - insertions
    - crotations
    - transrot
    - ssbonds and ssbondsdelete
    - links
    - substitutions
    - grafts
  - validate
  - pdb2pqr
  - md
  - manipulate
  - ligate
  - cleave
  - solvate
  - make_membrane_system
  - ring_check
  - terminate
- build-example
- fetch-example
- new-system
- wheretcl
- make-pdb-collection
- make-ligand-mol2
- desolvate
- make-namd-restart
- show-resources
- follow-namd-log
- mdplot
- modify-package
- setup-vmd
Examples
Configuration File Reference
- charmmff
  - user_pdbcollections
  - standard
    - rtf
    - str
    - prm
  - custom
    - rtf
    - str
    - prm
  - user_custom
    - searchpath
    - rtf
    - str
    - prm
    - segtypes
- psfgen
  - aliases
    - atom
    - residue
- namd
- paths
- tasks
API
- pestifer package
Tcl sources
Changelog

`deprecated3`¶

1-4scaling: oneFourScaling

Deprecated namd2 configuration parameters and their namd3 counterparts

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