Dear gromacs users I am trying to carry out a free energy perturbation to evaluate the difference in binding energy between two inhibitors of the same protein. I have read a lot of post but i did no understand how to create the topology file. have i to write a mixed pdb of the two inhibitors structure modifying the value of beta factor to -1;0,1 for disappearing and rising atoms and than to proceed by pdb2gmx ? Could someone please link a tutorial or a guide to follow. thanks in advance Antonio
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