i tried on charmm-gui site but an error appears, what should i do?
is there another way to calculate that?
Dear Soroush,
The solvation free energy calculation is given in detail by Lemkul's tutorial. Just follow the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
If you have any further question just let me know.
Hi Soroush,
You can calculate solvation free energies using AMBER and GROMACS by following these example tutorials:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html (for GROMACS)
http://ambermd.org/tutorials/advanced/tutorial9/index.html (for AMBER).
Essentially, what you need to do is construct a thermodynamic cycle and decouple your solute from the solvent (presumably, water), as is shown for the GROMACS tutorial above. Note that the AMBER tutorial describes transforming one solute into another, but you can easily modify it to decouple the solute from the solvent, i.e. transforming the solute into nothing. Based on my own experience, I suggest thermodynamic integration with soft-core potentials (available both in AMBER and GROMACS, see the reference manuals). If you have small, uncharged molecules, this is a pretty straightforward task. If, however, the molecules are fairly large, you may need to add a "volume correction"
ΔGcorrected = ΔGsimulation - kTln(V*/V1),
where V1 is the volume at full coupling and V* is the volume of a box of pure solvent, see
Article Extremely precise free energy calculations of amino acid sid...
Also, if the solutes are charged at the pH you are simulating, you will have to include more complicated corrections for the various artifacts in such simulations, see
Article Calculating the binding free energies of charged species bas...
I've never used CHARMM, but the basics are the same, I'm sure it has analogous features to perform the calculations, just consult the reference manual. Even if it doesn't for some reason, GROMACS is free, you can always install and run it.
You need to decouple your solute in
(a) the solvent
(b) a vacuum.
Take the difference in these values.
In addition to the papers already listed by Michael Shirts et al see
https://old.iupac.org/publications/pac/2004/pdf/7601x0231.pdf
For large system such as biomolecules, it difficult to calculate the solvation free energy precisely. For small molecules you can use quantum chemistry method such as DFT. Here is an article for your reference.
Article Quantum Chemical Calculation of pKas of Environmentally Rele...
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