Hello everyone:
Is there anyone who can perturb a portion of a molecule or protein when you do
FEP analysis ?
May you help me to solve the problem ?
Many Thanks!
Best regards
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Dear Gromacs users,
I am using Gromacs 5.0.6 with CHARMM27 forcefield. I want to do FEP analysis
and I did it based on this tutorials:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
.
But I just want to peturb some atoms of the protein, howeve
When we convert some atoms to a dummy atom (DUM) in a B state topology,
then does the Gromacs free energy code automatically take care of this
transformation in bonded terms (bond, angle, dihedral etc.) because we can
not define B state parameters corresponding to bonded terms of dummy atoms
in a t
