Member Site Forums Rosetta 3 Rosetta 3 – Applications a trouble during floppytail modeling Reply To: a trouble during floppytail modeling


    A) Donor and acceptor refer to hydrogen bond donation and accepting. For example, backbone carbonyl is an acceptor, N-H is a donor. (unless I have that backwards…)

    B) The electrostatics term in most of Rosetta, including FloppyTail, is the fa_pair term. I believe it is explained in the 2004 Rohl paper. Briefly, it was parameterized by examining the distribution of charged residues in a large database of structures. Charged residues in your structure are then graded based on how similar their distribution was to the reference distribution. For example, in the reference, it was uncommon to see two arginines near each other, so there is a penalty. It is common to see a glutamate and an arginine near each other, so there is a bonus. This handles electrostatic attraction/repulsion for the 20 canonical amino acids very efficiently, but as you can see has no idea what to do with calcium, as calcium wasn’t parameterized. There are score function terms available for “proper” coulombic, etc, electrostatics, but I’ve never used them, and I don’t know if they handle ions well. You can try looking at the code for hack_elec?