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michellab
Sire Molecular Simulations Framework
As py37 nears EOL, it's starting to cause issues as several dependencies (for Sire and BioSimSpace) are no longer being built against it. This PR drops support for py37 and...
Dear Sire Developers: This is an implementation of [soft bond potential ](https://pubs.acs.org/doi/10.1021/acs.jctc.6b00991), including the following changes: 1. Added a new perturbation type called ScalePerturbation to take care of the exclusion...
Reads qubekit output files (pdb/xml) and converts them to amber format (prm7/rst7) to use them with Sire usage: ~/sire.app/bin/qube_to_PrmRst -p PDB_FILE -x XML_FILE
Related to #411, we are unable to read another amber14sb related gromacs topology. This was generated in the same way as the topology in the other thread and will need...
The move to 2023 seems to have broken SOMD. The example below attempts to carry out an RBFE calculation on a protein-ligand system. I am using [feature_pmefep_2023](https://github.com/michellab/Sire/tree/feature_pmefep_2023) ; Sire version:...
Currently the full C++ backtrace is not exposed to the Python wrappers so cannot be parsed, e.g. by BioSimSpace. This is used in various places to provide additional contextual information...
From debugging [this](https://github.com/michellab/BioSimSpace/issues/369) BioSimSpace issue it is clear that our handling of HETATM records from PDB files is problematic and needs improving. Unfortunately the formatting of these records seems to...
Just a note regarding the release of `pymbar 4.0`, which has breaking API changes, as documented [here](https://pymbar.readthedocs.io/en/master/moving_from_pymbar3.html). We'll likely need to update the `analyse_freenrg` script if we want to use...
Issue for myself to remind me that we need to add support for CMAP terms and chamber files (and the CHARMM forcefield generally) to the AmberPrm parser. This will be...
When I run the FM1 tutorial example with the following execution: ``` (sire) spadavec@Crandall:~/itx/sire_example/ligandswap$ ligandswap -t0 rec_fmc.top -c0 fmc.30.crd -l0 FM1 -t1 rec_cti.top -c1 cti.30.crd -l1 CTI -C config ```...
