Hi, I would like to ask for advice regarding the handling of non-integral charges generated by modXNA.
In my system, I have a DNA chain containing three engineered residues. The partial charges for two of these residues are -0.999998 and -0.999999, which seems acceptable. However, the 3' terminal residue carries a charge of -0.679648, which deviates significantly from -1. (BTW, the standard 5' terminal residue carries a charge of -0.3079 and the total charge of the system is -0.067505 after neutralization attempt.)
Could you please advise on how to address this issue before proceeding with MD simulation?
Thank you for your attention.
Hi, I would like to ask for advice regarding the handling of non-integral charges generated by modXNA.
In my system, I have a DNA chain containing three engineered residues. The partial charges for two of these residues are -0.999998 and -0.999999, which seems acceptable. However, the 3' terminal residue carries a charge of -0.679648, which deviates significantly from -1. (BTW, the standard 5' terminal residue carries a charge of -0.3079 and the total charge of the system is -0.067505 after neutralization attempt.)
Could you please advise on how to address this issue before proceeding with MD simulation?
Thank you for your attention.