UCL-CCS BAC2 issues - Githubissues

UCL-CCS / BAC2

A tool for the automation of molecular simulations using multiple engines, focusing on binding affinity calculations

Apache License 2.0

4 stars 1 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

BAC2 Tutorials ？

#77 ErikZhang-9762 opened 2 months ago
0
ESMACS Jupyter Notebook

#76 GuoJeff opened 3 years ago
1
Automatic WSAS

#75 bieniekmateusz closed 4 years ago
3
Update and verify wang2012 wsas weights for leaprc.protein.ff14SB

#74 bieniekmateusz opened 4 years ago
5
Add basic unit tests for most WSAS

#73 bieniekmateusz opened 4 years ago
0
Investigate how Freesasa Classifier can be created programmatically

#72 bieniekmateusz opened 4 years ago
0
Consider switching to an offical freesasa wrapper

#71 bieniekmateusz closed 4 years ago
0
Transition to mdtraja sasa

#70 bieniekmateusz opened 4 years ago
1
Installation requirements in a new conda environment not documented

#69 dww100 opened 4 years ago
1
Running wsas-analysis.py

#68 bieniekmateusz closed 4 years ago
64
ipython notebook(s) to provide basic project description

#67 dww100 opened 6 years ago
0
Create chain/segment based access functions for ParmEd data structures

#66 dww100 closed 5 years ago
0
Obtain information for building from PDB header

#65 dww100 opened 6 years ago
1
Design figure from wiki missing

#64 dww100 opened 6 years ago
0
First draft of a WSAS calculator using a class

#63 dww100 closed 6 years ago
1
Constraints from B factors

#62 dww100 opened 6 years ago
1
Non-optional variable defaults

#61 kristofarkas closed 5 years ago
0
Water models in NAMD

#60 dww100 closed 6 years ago
2
Necessary enhancements of ParmEd to suit BAC requirements

#59 dww100 closed 5 years ago
5
WSAS features needed

#58 dww100 closed 5 years ago
1
WSAS branch checks

#57 dww100 closed 6 years ago
0
Integrate benchmarks

#56 kristofarkas opened 6 years ago
0
Document origin of Mobley example

#55 dww100 opened 7 years ago
0
Need to identify a proper license

#54 dww100 closed 6 years ago
3
Need to consider how to create and store extensions to previously run simulations

#53 dww100 opened 7 years ago
0
Amber FF versions change the atom types

#52 dww100 closed 7 years ago
0
Dependency management

#51 dww100 opened 7 years ago
0
Create force field information handling object

#50 dww100 opened 7 years ago
0
Redundant class definitions and import issues in simulate

#49 dww100 closed 7 years ago
0
Fix path management

#48 kristofarkas closed 7 years ago
0
Run free energy calculation on multicore cluster

#47 kristofarkas closed 7 years ago
5
Generic md class

#46 kristofarkas opened 7 years ago
0
Fix gromacs grps

#45 kristofarkas closed 7 years ago
1
Gromacs support in simulation

#44 kristofarkas closed 7 years ago
1
Implement equality and str for all classes

#43 kristofarkas opened 7 years ago
0
Encoding support

#42 kristofarkas closed 7 years ago
1
Add MMPBSA to Radical Script

#41 sjzasada closed 6 years ago
0
GROMACS normal model calculation validation

#40 dww100 closed 7 years ago
0
GROMACS normal mode calculation of configurational entropy

#39 dww100 closed 7 years ago
1
Investigate plausibility of using parmed in future to create hybrid ligands

#38 sjzasada closed 7 years ago
0
Update TIES hybrid tool

#37 sjzasada closed 7 years ago
1
Improve existing TIES hybrid ligand tool

#36 sjzasada closed 6 years ago
2
Library of present BAC protocols in BAC 2.0 format

#35 sjzasada closed 7 years ago
2
Prototype of PDB checker

#34 sjzasada closed 6 years ago
0
Draft specification for PDB checker

#33 sjzasada closed 6 years ago
0
Draft specification for raw PDB -> sim ready PDB module

#32 sjzasada closed 5 years ago
0
Fix AWS issue running large instances

#31 sjzasada closed 7 years ago
0
Benchmark GROMACS on Cartesius

#30 sjzasada closed 7 years ago
3
Design BAC AWS Control App

#29 sjzasada closed 7 years ago
0
Implement BAC analytics on AWS

#28 sjzasada closed 7 years ago
0