Extensively averaged electrostatic potential charges (xAvESP) is
an alternative method to RESP to determine QM charges for
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:
The files are in Amber prep.in format with Amber-99 atom types.