How to use our programs
- AIM and other electron-density tools
- Amber, general
- Amber, equilibration (sander)
- Amber, FEP relative
- Amber, FEP, charge
corrections
- Amber, FEP absolute
- Amber, FEP, hydration free
energy
- Amber, Gibbs (FEP or PMF)
calculations
- Amber, Jarzynski non-equilibrium
simulations
- Amber, parameters for a new molecule
- Amber, prep file for a new molecule
- Amber, SIIT - enhanced sampling with different solvent boxes
- APBS
- ArcViewer
- Autodock
- Big-QM
- C3SE machines
- calc_dg.py - calculate free
energies from Amber, Gromos, or Q simulations
- Calc QM/MM -2QM
- CD: burn a CD
- Chimera
- Cns
- ComQum
- ComQum with Orca
- ComQum-2QM
- ComQum-Exafs
- ComQum-NMR
- ComQum-polarised-Exafs
- ComQum-U
- ComQum-UX
- ComQum-X
- ComQum-X-2QM
- ComQum-X-Phenix
- Coot
- Cosmo calculation with Turbomole
- CCP4: Refmac, Coot, Edstat
- cvdw - calculate continuum van der
Waals energies with Amber
- Dbx - debugger
- Delphi
- Emma's programs
- Entropy
- Excited states with Gaussian or
Turbomole
- exttrjcrds - manipulate Amber MD
trajectory files
- FEFF
- Gaussian
- GCMC
- gen_syst1.py
- GIST
- Gnuplot
- gOpenMol
- Grid
- IFEFFIT
- iRED
- jmol
- Local programs
- Lunarc
- Lucris
- Maestro
- Maple
- Mead
- Mendeley
- Mopac
MM/PBSA
- MsOffice
- Molcas
- Molden
- Molsurf
- Mulfit
- Nemo (PMISP)
- NTSys
- O
- Open Access (LUP)
- OpenOffice
- Orca
- Phenix
- PON parameterisation
- Pymbar
- Pymol
- Q2MM
parameterisation
- Q - FEP energies
- Q - FEP energies for multiple
ligands
- QM/MM-FEP
- QM/MM-PBSA
- QRef
- QTCP
- QTCP-Lig
- QualStat
- Rasmol
- Resp: calculate charges for a new
molecule
- RMS fit with CNS and Rasmol
- RPQS
- Schrodinger suite
- Seam
- SIIT - enhance sampling with different solvent boxes (TIP3P and TIP4P-Ew)
- Solinprot (Torben)
- Spartan
- Sqm
- Swiss PDB viewer
- Titprot
- ThermoWat
- TmoleX
- Turbomole
- Umbrella sampling with Amber
- Unix: a few useful commands
- Viewmol
- Vim
- VMD
- WHAM and umbrella integration
- xAvESP charges
- xdrawchem