Dear all,
Binding free energy between ATP (GTP) and protein is calculated from the extracted snapshots of MD trajectory using AMBER and CHARMM force field, respectively. But their binding free energy order is different. Using AMBER force field, the order of binding free energy for ATP and GTP is consistent with experiments, although absolute binding energy has a large deviation from the experimental data. If CHARMM force field is used, the order is opposite which contradicts with the experimental results.
The binding free energy of Amber force field is calculated by MMPBSA.py script using Amber 11 and Ambertools 1.5, PB equation is solved by built-in program in Amber software. Toward CHARMM force field, MD trajectory is obtained by NADM 2.9 software. And then Chamber program in Amber is used to convert topology and force field files format. In this calculation, PB equation is solved by sander.APBS. Their input files are as follow:
#### Amber force file, Amber 11 and AmberTools1.5
&general
startframe=1, endframe=100, interval=1,
keep_files=2,strip_mdcrd=0,verbose=1,
/
&pb
istrng=0.1,
/
#### CHARMM force field Amber 11 and AmberTools 12
&general
startframe=1, endframe=100, interval=1,
keep_files=2,search_path=1,verbose=1,
/
&pb
istrng=0.1,sander_apbs=1,radiopt=0
Some previous researches show that binding free energy is independent of different force field. Whether did I make mistakes in binding energy calculation or something? Would you like to give me some help? Thanks in advance!
Best wishes
Duan Baogen
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Received on Mon Apr 01 2013 - 19:30:03 PDT
