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Acetone: Pre-Equilibration<br />
• Classical MD equilibra4on <br />
– relaxa4on near to a stable state <br />
– necessary in order to get closer to long relaxa4on 4mes, <br />
which are not accessable by ab ini4o MD methods alone <br />
• LEaP / XLEaP <br />
– creates a new system and generate force field files <br />
• reads AMBER force field informa4on / structural informa4on <br />
• constructs new molecules / residues / solva4on <br />
• generates topology and coordinate files to use in AMBER. <br />
– specify force field: xleap -s -f <br />
– e.g. leaprc.ff99SB: parameter files <br />
• parm99.dat : basic force field parameters (amino acids and some organic <br />
molecules <br />
• frcmod99SB: „Stony Brook“ modifica4on to ff99 backbone torsions <br />
• ff99: refers to a common force field for proteins for „general“ organic and <br />
bioorganic systems.
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