[gmx-users] Conformation free energy

[esther]

Hello,
I am studying a protein that has an amino acid modeled as a two-state rotamer in the crystal structure. I would like to quantify the probability of each conformation, so I thought of doing a FEP calculation. As I haven't seen much about this in the mailing lists, save for a D- L- amino acid calculation, I am wondering if there is a more obvious way to do this that I've overlooked? And if there isn't, what is the path to go from conformation 'A' to conformation 'B' in the top file?

Thanks in advance for your help,
Esther

Esther Caballero-Manrique
Graduate Teaching Fellow
Chemistry Department
1253 University of Oregon
Eugene, OR 97403-1253
(541) 346-2485