Hi everybody;
I have performed MD for protein and protein-ligand distinctively by Gromacs 4.5.7 but I didn't state the free energy computation parameters in .mdp file. Is there another way to avoid MD rehash for computing ligand binding energy?
Thanks
You can't get binding free energy from protein and protein-ligand systems, so the information you have is insufficient. You can calculate it most easily in one of three ways:
1. LIE method (you need protein-ligand and ligand-in-water systems)
2. PMF using the pull code (umbrella sampling)
3. Decoupling method (in which you also need the protein-ligand complex and ligand in water)
I meant Gibbs free energy as a thermodynamic parameter of binding.
Sorry for the confusion.
You can't get binding free energy from protein and protein-ligand systems, so the information you have is insufficient. You can calculate it most easily in one of three ways:
1. LIE method (you need protein-ligand and ligand-in-water systems)
2. PMF using the pull code (umbrella sampling)
3. Decoupling method (in which you also need the protein-ligand complex and ligand in water)
At the moment the most promising methods are based on thermodynamic cycles to estimate the free energy difference:
http://peds.oxfordjournals.org/content/8/11/1137.short
http://scitation.aip.org/content/aip/journal/jcp/89/6/10.1063/1.454895
Replica exchange methods give you a rather strong bias.
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