Comments (2)
I've also realised that our approach doesn't preserve atom numbering for multi-molecule systems. It's a pain, do we want to be compliant with the PDB, or should we only strive for this in single molecule systems, i.e. what will be used for parameterisation? Essentially, on fixing the issue I've found that the ordering in the PDB is now ascending, so it's useless for remapping coordinates with SOMD.
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Right, I've added an option to write the PDB using the original atom numbers from the system, which makes the SOMD re-mapping work. This is activated by passing {"use_atom_numbers" : True}
as a property map. These are horrible hacks on top of horrible hacks, but will hopefully be entirely redundant when SOMD2 arrives.
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Related Issues (20)
- [BUG] perturbable_constraint validation doesn't check for underscores HOT 1
- minimisation().commit() and dynamics().commit() return the wrong type
- [BUG] BSS fails to add ligand resname to PDB when saving non-cognate system HOT 6
- [BUG] Sire disables DEBUG level from global logger
- [BUG] ResIdxAtomCoordMatcher segfaults if residues contain different numbers of atoms
- Sire fails to compile with python 3.12 HOT 5
- [BUG] Circular import issue and small typo in Sire-EMLE tutorial HOT 5
- [BUG?] Does the alanine dipeptide test system have a mixture of combining rules? HOT 5
- [BUG] Reduced triclinic boxes can't be used with OpenMM C++ API
- [BUG] AmberPrm reader reorders atoms when molecules are not contiguous in the file HOT 3
- [BUG] Mol2 parser element inference isn't robust
- Preserve PDB information when interconverting with RDKit
- Add support for reading Gromacs FEP topology files HOT 2
- [BUG] - Iron not recognised as a biological element
- Add square root, power etc to units HOT 2
- Not recognising amide bond? HOT 1
- [BUG] create_from_pertfile uses next instead of continue when skipping atoms that don't match the perturbation template HOT 2
- [BUG] Update cmake version as upcoming deprecation HOT 2
- Add "auto" constraints and then update tutorial HOT 1
- [BUG] sire.morph.create_from_pertfile doesn't assign different element properties to the end states
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