The discovery that ATP can prevent the aggregation of proteins and enhance their stability sparked significant interest in understanding the interactions between ATP and proteins. All-atom molecular dynamics simulations provide detailed insight into the underlying mechanism, while an appropriate force field must be developed. Existing force fields accurately describe the conformations of polyphosphates, but are not suitable for simulations at high ATP concentrations, because excessive self-aggregation occurs. We address this issue by scaling the atomic charges of the ATP anion and its counterions. The experimentally observed aggregation can be reproduced by using a scaling factor of 0.7 applied to the phosphate moiety of ATP and its counterions. This charge scaling is in line with a physically motivated implicit account of polarization effects, which is increasingly applied in simulations of ionic systems.
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