Hello,
I'm studying a DNA helix in two different conformations and would like to compare the free energies. For this purpose I'm using the mmpbsa perl script supplied with Amber9.
To calculate the nonpolar free energy contribution to the solvation energy in the PB method two parameters CAVITY_SURFTEN and CAVITY_OFFSET are needed. In the the examples included with Amber9 (amber9/src/mm_pbsa/Examples/03_MMPBSA_Binding/mm_pbsa.in) and in Tutorial A3 it is stated in the remarks in the script to use values of 0.04356 and -1.008, respectively, for NOPT=1 and RADIOPT=0, but in the input files in both the examples and in the tutorial values of 0.0072 and 0.00, respectively, are used. Can anyone help to shed light on this?
Similarly, the parameters SURFTEN and SURFOFF in the GB method are a cause for confusion. For IGB=2, the paper by Gohlke et al., J. Comput. Chem. 2004, 25, 238 recommends to use 0.500 and 0.00, respectively, whereas the examples and the tutorials again use the values of 0.0072 and 0.00, respectivly. What would be the appropriate parameters for IGB=2?
Furthermore I have two other questions that puzzles me:
- Is the option MS obsolete since the nonpolar part of the solvation free energy is now calculated in both the PB and the GB options?
- Can the python script mmpbsa.py be used in a case with only a single molecular species, or is it just for receptor, ligand, complex cases?
Cheers,
Michael Petersen
__________________________________
Michael Petersen,
Dept. of Physics and Chemistry,
University of Southern Denmark,
Campusvej 55,
5230 Odense M,
Denmark.
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Received on Wed Nov 03 2010 - 15:00:04 PDT
