Slides

Acetone: XLEaP
– graphical user interface
– load par4al charges into XLEaP: loadAmberPrep
– load other force field: loadAmberParams gaff.dat
• GAFF: force field for general organic molecules
– load addi4onal bond lengths and bond angle parameters:
loadAmberParams acetone.frcmod
(calculated with parmcal)
– edit unit
• unit: object containing all the informa4on for the calcula4on using AMBER
– check unit
• checks bond lengths, total charge, missing parameters, close contacts, …
– save data into files readably by AMBER:
saveAmberParm unit topologyfilename coordinatefilename
• topology file : connec4vity, atom names, atom types, residue names, and charges
• coordinate file : cartesian atomic coordinates
BOND
c-o 643.701 1.216
... force equilibrium
ANGLE
constant value
o-c-c3 67.993 121.723
...