On Wed, Nov 3, 2010 at 5:58 PM, Michael Petersen <mip.ifk.sdu.dk> wrote:
> 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?
>
I agree that these are problematic... I'd suggest using the values that
people have tried to systematically validate for similar systems in the
literature, if that's available. Sorry I can't be of more help since I have
not done any kind of systematic study about this.
> 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?
>
No, because it still gives slightly different answers. I'm not familiar
with the algorithm that MS uses to calculate the molecular surface, but I've
seen that the results differ. I've always been content to use PB's and GB's
molecular surface calculations.
> - 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?
>
It's currently only complex, receptor, and ligand cases, but it's being
expanded so that it will perform calculations on only a single species.
(I'm aware that this doesn't help you now, but it at least lets you know
we're working on it).
Good luck!
Jason
>
> Cheers,
> Michael Petersen
>
> __________________________________
> Michael Petersen,
> Dept. of Physics and Chemistry,
> University of Southern Denmark,
> Campusvej 55,
> 5230 Odense M,
> Denmark.
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 03 2010 - 16:30:04 PDT
