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AMBER interface
Basic interface for MM calculations using AMBER package (commercial). The interface should work with AMBER versions 7 to 10 (the latest one). It uses tleap utility to prepare topology file for the calculation, what requires following setup in cuby input:
- Leaprc file that loads the forcefield must be specified. Default one is read from config file, custom leaprc can be specified using keyword leaprc.
- Geometry for cuby calculation must be in PDB format, with proper naming of atoms and residues. The order of atoms must be the same leap uses. Best way to prepare such a file is to open geometry in leap and save it to PDB.
New in cuby3
The interface no longer needs modified AMBER code to run. Now, gradients are read from debugging output of sander.