[gmx-users] free energy perturbation

antonio antonio.coluccia at uniroma1.it
Thu Nov 25 13:53:57 CET 2010

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

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