Collection of mostly python code for molecular visualization, QM/MM, FEP, etc. Very long-term goal is something like enzyme design. Intended for interactive use from standard python prompt.
- 3D visualization of molecular geometry, orbitals, ESP, etc.
- fast OpenGL volume and isosurface rendering
- oriented toward analysis and debugging of calculations rather than presentation (for that, try molstar)
- QM/MM driver supporting electrostatic embedding with various charge shifting schemes
- DLC/HDLC/Redundant internal coordinates
- transition state search (Dimer method, Lanczos method), reaction path optimization (NEB)
- read/write .pdb, .xyz (TINKER/generic), GAMESS and NWChem files
- model creation and setup: build polypeptides, add hydrogens and bonds, mutate residues, solvate
- free energy methods: FEP, BAR, umbrella sampling
- If an example in projects/ or test/ looks promising, try using that as a starting point ... currently, most of the examples are outdated or work-in-progress. Open an issue describing what you're interested in doing and I'll help with getting started.
- add
import pdb; pdb.set_trace()to step line by line - see "Examples" in test/vis_test.py for standalone visualization examples or
- Cut and paste what you need: code is kept as self-contained as possible
- opt/dlc.py: delocalized internal coordinates (DLC) and hybrid DLC; useful for geometry opt. w/ constraints
- opt/lbfgs.py: gradient-only BFGS and L-BFGS optimizers (i.e., no line search)
- opt/neb.py: nudged elastic band (reaction path optimization)
- opt/dimer.py: Dimer and Lanczos methods (transition state search)
- qmmm/resp.py: RESP/CHELPG charge fitting (only harmonic restraints currently)
- mm.py: slow but simple MM energy and gradient for AMBER-type force field (and Hessian for Coulomb and LJ), GBSA implicit solvation energy
- molecule.py: atom selection, molecule alignment
- fep.py: simple FEP, BAR free energy calculations; MM-GBSA binding energy
- analyze.py: solvent accessible surface area, hydrogen bonding (DSSP), secondary structure
- model/build.py: build polypeptides, add hydrogens and bonds, mutate residues, set rotamers
- model/prepare.py: build solvent box, solvate, neutralize, check geometry
- Python 3 w/ scipy and numpy (should mostly still work with Python 2.7)
- OpenMM - molecular mechanics calculations
- PySCF - quantum chemistry calculations
See misc/chem-inst.sh for setup on Debian/Ubuntu
Optionally:
- openmmtools - free energy calculations
- AmberTools - small molecule parameterization (GAFF)
- TINKER - molecular mechanics calculations
- GAMESS (US) or NWChem - quantum chemistry calculations
- https://github.com/cclib/cclib - for reading GAMESS and NWChem output
Credit to chemlab (3D camera, some shaders) and speck (some shaders), among others.
1MCT.pdb shown with backbone ribbon, MM atoms as lines, QM atoms as sticks, and components of QM/MM force on each atom as yellow, cyan, magenta cylinders.
