6. Multi-State RESP Fitting

The MultiResp subpackage contains a series of useful classes for handling Amber parm7 files, and for calculating multi-state RESP fitting to obtain charges for MD simulation forcefields. The primary use case of this package is to be a combination of ligandparam.stages.gaussian.StageGaussianRotation stage and the ligandparam.stages.resp.StageMultiRespFit stage.

Available Stages:

• 6.1. ligandparam.multiresp.mdinutils
  • AmberCmd
  • Disang1D
  • Disang2D
  • Mdin
• 6.2. ligandparam.multiresp.parmhelper
  • BASH
  • Computer
  • CopyParm()
  • Fragment
  • FragmentedSys
  • GetSelectedAtomIndices()
  • GetSelectedResidueIndices()
  • ListToSelection()
  • MakeUniqueAngleParams()
  • MakeUniqueBondParams()
  • MakeUniqueDihedralParams()
  • OpenParm()
• 6.3. ligandparam.multiresp.residueresp
  • ResidueResp
• 6.4. ligandparam.multiresp.endstate
  • EndState
• 6.5. ligandparam.multiresp.intermolequiv
  • IntermolEquiv
  • RespMol
• 6.6. ligandparam.multiresp.functions
  • WriteFitSh()
  • WriteFrcmodObj()
  • WriteLeapSh()
  • WriteMaskedFrcmod()
  • statisticalInefficiency()
• 6.7. ligandparam.multiresp.respfunctions
  • GetAtomsBondedToIdx()
  • GetAvgStdDevAndErr()
  • GetEquivHydrogens()
  • GetEquivNonbridgeOxygens()
  • GetResidueNameFromAtomIdx()
  • ReadGauEsp()
  • ReadGauOutput()
  • ReadNextRespCharges()
  • ReadOrMakeGauEsp()
  • RunGauEsp()
  • WriteArray8()

6.8. Attribution

This mini-core package is adapted from the (unreleased) parmutils package originally developed by Prof. Tim Giese at Rutgers University. These functions and classes have been adapted to work with the ligand_param package, but have otherwise been left unchanged (except for documentation additions).