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Commit History

Commits on Jun 3, 2024

• update BF4 anion for amoebail22 ionic liquid parameters

  jayponder

  committed
  d6692f5

Commits on May 18, 2024

• update surface.f & volume.f to use unionball for more cases

  jayponder

  committed
  3072c66

• modifications to unionball to handle symmetric cases

  jayponder

  committed
  d6aed01

Commits on May 12, 2024

• safeguard mutate atoms to be within allocated atom range

  jayponder

  committed
  4c283a5

Commits on May 7, 2024

• update output format of implicit solvation parameters

  jayponder

  committed
  ecbd929

Commits on May 6, 2024

• fix bug in scaling of KUNDROT volume derivatives for GK

  jayponder

  committed
  2e2a2ae

Commits on May 5, 2024

• update documentation & code to Tinker 8.11.2 release

  jayponder

  committed
  8a8098d

Commits on May 4, 2024

• add writing GK/PB dipoles to induced dipole file

  jayponder

  committed
  afdc820

• update Makefiles for implicit solvent binding free energies

  jayponder

  committed
  0814ff2

Commits on May 2, 2024

• infrastructure for implicit solvent free energy calculations

  jayponder

  committed
  bad6bea

Commits on Apr 30, 2024

• fix writing of induced dipole files during optimization

  jayponder

  committed
  112e51c

Commits on Apr 14, 2024

• patch cation.run in /test to run BAR from /bin directory

  jayponder

  committed
  9e8e906

Commits on Apr 13, 2024

• reorganization of area & volume calling interfaces

  jayponder

  committed
  39c5750

Commits on Apr 11, 2024

• standardize calling arguments for area/volume routines

  jayponder

  committed
  5bd8e51

• correct text formatting across several source files

  jayponder

  committed
  1b6d75e

Commits on Apr 10, 2024

• format & comment updates to UnionBall area & volume

  jayponder

  committed
  5c156e9

• cleanup comments in UnionBall area & volume code

  jayponder

  committed
  d10cb91

Commits on Apr 9, 2024

• minor updates to UnionBall-based area & volume

  jayponder

  committed
  25f5f65

Commits on Apr 8, 2024

• bigger arrays in Connolly to allow larger structures

  jayponder

  committed
  de10388

• modify chksymm routine to add center of inversion

  jayponder

  committed
  247e3d7

• patch to apply atom weights to volume for GB & GK

  jayponder

  committed
  b0f8782

• move to Tinker 8.11.1; UnionBall code & many updates

  jayponder

  committed
  428faa9

Commits on Feb 8, 2024

• fix PDBXYZ bug for terminal GLY HA in multiple chains

  

  Jay Ponder

  committed
  034b705

Commits on Feb 1, 2024

• fix bug in reading wildcard parameters from keyfile

  

  Jay Ponder

  committed
  c9698d2

Commits on Oct 13, 2023

• adjust NCRDSAV in DCD files for compatibility with MDAnalysis

  jayponder

  committed
  b043c26

Commits on Oct 12, 2023

• patch the output of SOLUTE records read from keyfiles

  jayponder

  committed
  22e547a

Commits on Oct 6, 2023

• fix PDBXYZ bug for N-terminal PRO in 2nd and later chain

  jayponder

  committed
  7855bc8

Commits on Oct 1, 2023

• update documentation for new implicit solvation keywords

  jayponder

  committed
  c2f4366

• cleanup GK solvation using Corrigan JCTC cavity term

  jayponder

  committed
  fa87b83

Commits on Sep 22, 2023

• implement fixing dipoles by atom in POTENTIAL fitting

  jayponder

  committed
  97d0102

Commits on Sep 21, 2023

• further cleanup of GK neck correction routines

  jayponder

  committed
  4576f81

Commits on Sep 19, 2023

• further GK update to amoebapro13.prm and amoebanuc17.prm

  jayponder

  committed
  cd2b295

• update to correct GK parameters for amoebabio18.prm

  jayponder

  committed
  92528f7

Commits on Sep 15, 2023

• update to include Rae Corrigan GK methodology for proteins

  jayponder

  committed
  f95092a

Commits on Jun 16, 2023

• add virial contribution for GK in the egk1 routine

  jayponder

  committed
  b6a58df

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