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UCL-CCS
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TIES
Topology Superimposition based on joint graph traversal
MIT License
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Installation: check how to best attach data ie structure repository
#182
bieniekmateusz
closed
2 years ago
0
Further investigation into zero-sum with L6
#181
bieniekmateusz
closed
2 years ago
12
Bootstrap dGs to understand the gain as a function of a number of replicas
#180
bieniekmateusz
closed
4 years ago
0
Elaborate the explanation of -mismatch in the documentation
#179
bieniekmateusz
closed
2 years ago
0
Allow -mismatch to use an asterisk
#178
bieniekmateusz
closed
2 years ago
0
Add test cases for the interface -match -mistmach etc
#177
bieniekmateusz
closed
2 years ago
0
add continuous integration and testing dataset in the repository
#176
bieniekmateusz
closed
2 years ago
0
TIES and conda - add conda specific information to pip so that it links it against ambertools
#175
bieniekmateusz
closed
2 years ago
0
Improve the installation protocol
#174
bieniekmateusz
closed
4 years ago
1
Standardise bootstrapping and data extraction
#173
bieniekmateusz
closed
2 years ago
0
Generalise ddg to allow including replicas from several different directories
#172
bieniekmateusz
closed
2 years ago
0
TIES - manual verification of potential energy terms
#171
bieniekmateusz
closed
2 years ago
0
Replace your table with tabular in ddg
#170
bieniekmateusz
closed
2 years ago
0
Organise ddg data into pandas and save it after parsing.
#169
bieniekmateusz
closed
2 years ago
0
VDW being not linear, and its relationship to ELE
#168
bieniekmateusz
closed
2 years ago
0
Consider only the prod.alch file in deciding on whether the sim is done.
#167
bieniekmateusz
closed
2 years ago
0
Change error message to error output
#166
bieniekmateusz
closed
2 years ago
0
separate the creation of the two ligands with ambertools to keep their logs
#165
bieniekmateusz
closed
2 years ago
0
ambertools in subprocess.run does not throw errors even if it logs errors
#164
bieniekmateusz
closed
2 years ago
0
Argparse: consider the case where one file is .mol2 and one file is .pdb etc
#163
bieniekmateusz
closed
2 years ago
0
Suppress warning for .mol2 instead of the current workaround
#162
bieniekmateusz
closed
4 years ago
0
Account for the .frcmod penalty numbers
#161
bieniekmateusz
closed
2 years ago
0
Instead of renaming all atoms before, rename them after only after knowing which have to be unique.
#160
bieniekmateusz
closed
2 years ago
0
Create an interface for TIES
#159
bieniekmateusz
closed
2 years ago
0
Create symbolic links to the NAMD input in order to have one centralised control over all replicas.
#158
bieniekmateusz
closed
2 years ago
0
Use antechamber in their own directories to keep the log
#157
bieniekmateusz
closed
2 years ago
0
Separate pipelines in TIES to allow single deltaG
#156
bieniekmateusz
closed
2 years ago
0
Switch to Tabulate for ddg results
#155
bieniekmateusz
closed
2 years ago
0
Allow to determine the charge of the ligand/protein using propka - and others
#154
bieniekmateusz
closed
2 years ago
0
Poor performance of L6-L14 ptp1b (and others)
#153
bieniekmateusz
closed
4 years ago
76
Adapt Pandas and generate latex reports automatically
#152
bieniekmateusz
closed
2 years ago
0
Investigate the output from the simulations to ensure that the energies make sense
#151
bieniekmateusz
closed
2 years ago
0
Migrate TIES to symbolic links
#150
bieniekmateusz
closed
4 years ago
2
Analysis Pipeline: transitions to Pandas and use headers to manage created data
#149
bieniekmateusz
closed
4 years ago
2
Consider BOINC for TIES/ESMACS
#148
bieniekmateusz
closed
2 years ago
0
Look into ambertools free energy pack
#147
bieniekmateusz
closed
2 years ago
0
Charges nullified
#146
bieniekmateusz
closed
2 years ago
1
Transitioning to parmed to avoid "merging frcmod"
#145
bieniekmateusz
closed
2 years ago
1
OpenMM and potential energy derivative processing - atom attribution
#144
bieniekmateusz
closed
2 years ago
0
Plot the data such that it is easy to attribute where most of the ddG difference comes from
#143
bieniekmateusz
closed
2 years ago
0
Should NAMD disappear the bonds and annihilate atoms?
#142
bieniekmateusz
closed
4 years ago
0
Transition to VECMA: try Pilot, Fabsim, UQ etc
#141
bieniekmateusz
closed
2 years ago
0
do not allow to overwrite files - make a backup copy of them
#140
bieniekmateusz
closed
2 years ago
0
Should we neutralise and solvate each replica separately?
#139
bieniekmateusz
closed
2 years ago
0
Eq protocol: increase the temperature step by step
#138
bieniekmateusz
closed
2 years ago
0
The wrong number of ions - MCL1 L1 L8
#137
bieniekmateusz
closed
4 years ago
1
Problem with charges in the system
#136
bieniekmateusz
closed
2 years ago
1
Add an extra check for the charges
#135
bieniekmateusz
closed
2 years ago
0
Check the journals for the best up-to-date NAMD MD protocol
#134
bieniekmateusz
closed
2 years ago
0
Use a better spline for energy calculation
#133
bieniekmateusz
closed
2 years ago
0
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