Hi, all GROMACS specialists. I have a question about ligand simulation in water. In binding free energy calculations of ligand and protein, we need two simulation systems, one
- -protein+ligand in water and second is
- -ligand in water.
My question is that the ligand in water simulation same as simulation for solvation free energy or is it different from that.
For solvation free energy of ligand I follow bevan lab's protocol.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
Can I use that for binding free energy?
Note that my tutorial is not a complete solvation free energy; it is just the van der Waals part of the transformation. You'd need to do additional calculations to transform charges. But yes, the general protocol is what you need for the ligand transformation in water.
thank you Sir for your reply.
In that tutorial you also showed how to use coulomb lambdas. I follow these steps. is it okay.
Yes, a full annihilation of both van der Waals and electrostatic terms would constitute a solvation free energy.
Entropy: A concept that is not a physical quantity
https://www.researchgate.net/publication/230554936_Entropy_A_concept_that_is_not_a_physical_quantity
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