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What parameters (force-field, etc) are used to set up AMBER topology and coordinate files?

April 26, 2017amber coordinate files force-field parameters Topology Used

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What parameters (force-field, etc) are used to set up AMBER topology and coordinate files?

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parm99 (Wang and Kollman 2001) with modifications ff99SB (Hornak et. al. 2006) and parmsbc0 (Perez et. al. 2007); Bondi radii set; TIP3P water box with a 10A buffer between the molecule and the box boundary. All disulfate (CYX-CYX) bonds found in the structure are set. Na+ and Cl- counterions are added to neutralize the system (e.g. if the molecule’s charge is +5 at the given pH, 5 Cl- ions are added using Leap’s “addions” command). Also note that in the current implementation, the terminal residues are always left in their standard protonation states, even though their pKs may indicate otherwise.