I have used APBS to calculate ploar sovation energy for protein after the MD simulation. In MD simulation, I treat the system with 150mM NaCL, and tip3p water. For APBS run, I am a little confused about whether I should define the ion concentration in the APBS .in file. Because actually the input pqr file I used for APBS does not include ion and water.
Thank you very much.
Graduate Student at
School of Engineering
Department of Biomedical Engineering
University of Alabama at Birmingham