deGrootLab / pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

deGrootLab/pmx Issues

Hydrogen mapping
Updated 11 days ago
Repartitioning dummy atom hydrogen mass
Updated 11 days ago3
add special ions
Updated 5 months ago
charmm36mut force field failed with Fatal error: Atom type ON2 (residue TPO) not found in atomtype database
Updated 6 months ago2
How to interpret wplots?
Updated 7 months ago1
the calculation of transitions between ligands with different total charges
Updated 8 months ago2
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
Updated 9 months ago3
Confusion in [ dihedrals ] section in hybrid topology
Updated 8 months ago1
Is it possible to run non-equilibrium FEP from pre-equilibrated end points?
Updated 10 months ago2
Request to add branch
Updated a year ago
Controlling how many threads/cores are used when running PMX command line
Closed a year ago2
Using hydrogen mass repartitioning and non-equilibrium FEP.
Closed a year ago14
Why does PMX ligandHybrid fail for this specific ligand?
Closed 2 years ago2
Gromacs 4.6 with an alternative soft-core function
Closed 2 years ago8
Using pmx with parmed generated gromacs topologies
Closed 2 years ago4
develop branch - Multiple indentation errors
Updated 2 years ago
Error in ligand_alchemy.py
Closed 2 years ago2
Error with Zn atom
Updated 2 years ago1
IndexError: list index out of range
Closed 3 years ago2
Error in atom.py
Updated 3 years ago
Python 3 error loading pickle
Updated 3 years ago
Which license? LGPL or GPL?
Updated 3 years ago
Writing multifile topology fails to parse path
Closed 3 years ago3
Cannot do mutation with certain reside
Closed 4 years ago2
option to generate whole DNA/RNA library
Updated 6 years ago
add script to test ff libraries
Updated 6 years ago
py3 compatibility
Updated 5 years ago2
ff libraries in develop are unchecked/untested (and likely problematic)
Updated 9 months ago1