deGrootLab/pmx

Issues

• Confusion in [ dihedrals ] section in hybrid topology

  #38 opened a year ago by wagleswapnil
  3

• Hydrogen mapping

  #47 opened 3 months ago by pbuslaev
  2

• Add --no-mass-change flag to `atomMapping` script

  #49 opened 3 months ago by pbuslaev
  0

• Repartitioning dummy atom hydrogen mass

  #45 opened 8 months ago by DreamCykl
  3

• add special ions

  #44 opened 8 months ago by Lyn-666
  0

• charmm36mut force field failed with Fatal error: Atom type ON2 (residue TPO) not found in atomtype database

  #43 opened 10 months ago by Lyn-666
  2

• How to interpret wplots?

  #42 opened 10 months ago by DreamCykl
  1

• the calculation of transitions between ligands with different total charges

  #40 opened a year ago by hiro0426
  2

• ff libraries in develop are unchecked/untested (and likely problematic)

  #5 opened 7 years ago by matteoaldeghi
  1

• AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

  #39 opened a year ago by JiangXu123
  3

• Is it possible to run non-equilibrium FEP from pre-equilibrated end points?

  #37 opened a year ago by DreamCykl
  2

• Request to add branch

  #36 opened a year ago by woefulblock401
  0

• Controlling how many threads/cores are used when running PMX command line

  #34 opened a year ago by noahharrison64
  2

• Using hydrogen mass repartitioning and non-equilibrium FEP.

  #33 opened 2 years ago by noahharrison64
  14

• Gromacs 4.6 with an alternative soft-core function

  #31 opened 2 years ago by noahharrison64
  8

• Why does PMX ligandHybrid fail for this specific ligand?

  #32 opened 2 years ago by noahharrison64
  2

• Using pmx with parmed generated gromacs topologies

  #30 opened 2 years ago by aminsagar
  4

• develop branch - Multiple indentation errors

  #26 opened 2 years ago by mdpoleto
  0

• Error in ligand_alchemy.py

  #24 opened 3 years ago by qqq12a
  2

• Error with Zn atom

  #23 opened 3 years ago by almeida85
  1

• IndexError: list index out of range

  #22 opened 3 years ago by biotech70
  2

• Error in atom.py

  #19 opened 3 years ago by etiur
  0

• Python 3 error loading pickle

  #18 opened 3 years ago by cescgina
  0

• Which license? LGPL or GPL?

  #17 opened 3 years ago by stain
  0

• Writing multifile topology fails to parse path

  #14 opened 3 years ago by bertadenes
  3

• Cannot do mutation with certain reside

  #13 opened 4 years ago by xiki-tempula
  2

• py3 compatibility

  #6 opened 7 years ago by matteoaldeghi
  2

• option to generate whole DNA/RNA library

  #8 opened 6 years ago by matteoaldeghi
  0

• add script to test ff libraries

  #7 opened 7 years ago by matteoaldeghi
  0