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80 Open 973 Closed
80 Open 973 Closed
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Issues list

Precentered is ignored when atom_indices != None
#1966 opened Jan 8, 2025 by d-beltran
Calculate sasa to specific residues/pocket
#1964 opened Jan 4, 2025 by H-EKE
Residue number overflow in OpenMM
#1963 opened Dec 18, 2024 by Ruibin-Liu
3
Atom number overflow not treated properly
#1962 opened Dec 18, 2024 by Ruibin-Liu
md.join is extremely slow and memory inefficient
#1961 opened Dec 16, 2024 by k9cdt
1
Store formal charges from OpenMM 8.2+
#1956 opened Dec 6, 2024 by mattwthompson
Including additional arrays in H5MD trajectory files?
#1955 opened Dec 2, 2024 by orionarcher
_ZSt28__throw_bad_array_new_lengthv
#1954 opened Nov 29, 2024 by weigcdsb
5
UnicodeEncodeError: 'ascii' codec can't encode characters in position 12-16: ordinal not in range(128)
#1953 opened Nov 29, 2024 by AthenACHY
1
Test on Python 3.13
#1952 opened Nov 25, 2024 by mattwthompson
Type annotations
#1950 opened Nov 21, 2024 by mattwthompson
Issues with wernet_nilsson hbond counting in trajectory
#1948 opened Nov 15, 2024 by PowersPope
atom_slice loses information on chain IDs
#1947 opened Nov 14, 2024 by jakublala
1
mdtraj.load() to read various non-standard spec PDB files (ReFix)
#1945 opened Nov 13, 2024 by PowersPope
1
6
.dcd file size restriction?
#1941 opened Oct 25, 2024 by vishlashkari
2
Trajectory.atom_slice uses different orders for coordinates and topology
#1937 opened Oct 18, 2024 by pbuslaev
Add deuterium to atomic radii used in Shrake-Rupley?
#1935 opened Oct 16, 2024 by rachitk
1
mistake in latest mdtraj
#1931 opened Sep 29, 2024 by hangqijie
7
Preserve bond orders when writing out/reading in HDF5 trajectory files api For changes to the way the user interacts with the codebase wishlist
#1930 opened Sep 23, 2024 by SHZ66
1
No obvious link to GitHub from the documentation
#1927 opened Sep 18, 2024 by stefanor
3
make_molecules_whole fails when bonds are not well ordered
#1925 opened Sep 9, 2024 by eruijsena
1
7
Notebook examples failing in documentation
#1924 opened Aug 30, 2024 by ekiefl
3
mdtraj hydrogen bond analysis
#1921 opened Aug 28, 2024 by Bhavi8701
Issue with mdtraj.kabsch_sander Returning Zero Energies for DNA Hydrogen Bonds
#1915 opened Aug 14, 2024 by ShenWenHuibit
Error converting amber .nc to gromacs .xtc
#1914 opened Jul 22, 2024 by xavgit
3
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