We addressed some of these electrostatics problems (Xray artefact like presence of ions, crystal packing, etc) a long time ago. Feel free to look at:
Improving macromolecular electrostatics calculations. Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Protein Eng. 1999 Aug;12(8):657-62 and Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Nielsen JE, Vriend G. Proteins. 2001 Jun 1;43(4):403-12. Greetings Gert On 05/10/2015 12:37 PM, Andre Godoy wrote: Dear users. I'm comparing surface charge of a structure with its homologous (85% seq ID), and noted that APBS suggest completely opposite charge distribution (exactly what I expected, since despite its similarity molecules have opposite biochemical profile) But since molecules are quite similar, I'm not convinced that charge distribution can be that different. Considering that AA is basically the same, what other factors can be influencing APBS charge calculations? (Ex: rotamers position, crystal packing, crystallization conditions, etc) best, Andre Godoy IFSC - University of Sao Paulo - Brazil Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
