## apbs-users

 [Apbs-users] about binding energies from APBS From: Yongqi Huang - 2010-09-20 13:28:50 Attachments: Message as HTML Hi apbs user, I am not familiar with theoretical calculation, but I am still interested in using APBS to analyze molecular interactions. Currently, I am trying the APBS examples. I have one basic question about the results. The output binding energies=complex - mol1 - mol2. In some case, e.g., actin-dimer, the binding energy is ~104 kJ/mol (positive); while in some case, e.g., hca-ligand, the binding energy is ~52 kJ/mol (negative). What is the exact meaning of these results? Do they mean dimerization of actin is electrostatically unfavorable? Thank you very much. Yongqi Huang 2010-09-20 Yongqi Huang
 Re: [Apbs-users] about binding energies from APBS From: Baker, Nathan - 2010-09-20 16:04:30 Attachments: Message as HTML Hi Yongqi - It is important that you familiarize with the theoretical background, at least at a basic level. There are several excellent review articles available; please let us know if you need specific suggestions. Thanks, __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory From: Yongqi Huang [mailto:yqhuang@...] Sent: Monday, September 20, 2010 6:10 AM To: apbs-users Subject: [Apbs-users] about binding energies from APBS Hi apbs user, I am not familiar with theoretical calculation, but I am still interested in using APBS to analyze molecular interactions. Currently, I am trying the APBS examples. I have one basic question about the results. The output binding energies=complex - mol1 - mol2. In some case, e.g., actin-dimer, the binding energy is ~104 kJ/mol (positive); while in some case, e.g., hca-ligand, the binding energy is ~52 kJ/mol (negative). What is the exact meaning of these results? Do they mean dimerization of actin is electrostatically unfavorable? Thank you very much. Yongqi Huang 2010-09-20 ________________________________ Yongqi Huang