xAvESP charges

Extensively averaged electrostatic potential charges (xAvESP) is an alternative method to RESP to determine QM charges for biomolecules.

The method was first described and tested in [P. Söderhjelm, U. Ryde (2009) "Conformational dependence of charges in protein simulations", J. Comput. Chem., 30, 750-760; DOI: 10.1002/jcc.21097]. These charges were obtained from 20 snapshots from MD simulations of avidin (full tetramer) with seven different biotin analogues (QM calculations from [A. Weis, K. Katebzadeh, P. Söderhjelm, I. Nilsson, U. Ryde (2006) “Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field”, J. Med. Chem., 49, 6596-6606; DOI: 10.1021/jm0608210]).

Then, similar charges were obtained for five additional proteins (the carbohydrate-recognition domain of Galectin-3 (two different crystal structures and five different ligands), factor Xa, hisactophilin (three different protonation states of all 21 histidines), haloalkane dehalogenase, and the GCN4 leucine zipper) [S.Genheden, P. Söderhjelm, U. Ryde (2010) "Transferability of conformational dependent charges from protein simulations" J. Chem. Theory Comput., submitted]. The charges were shown to be stable and transferable between the various proteins. Moreover, charges are now available for all the 20 normal amino acids, including their amino- and carboxy-terminal variants, as well as alternative protonation states for His, Asp, Glu, Lys, Arg, Cys, and Tyr.

These, charges xAvESP2 are avaliable here in three files:

all_amino_xavesp2.in - normal residues
all_aminoct_xavesp2.in - carboxy-terminal residues
all_aminont_xavesp2.in - amino-terminal residues

The files are in Amber prep.in format with Amber-99 atom types.