Hi, I am trying to conduct a ligand-only TI energy
perturbation using sander (Amber 8.0) based on prof.
Case's tutorial. I used the same forward input files
for the reverse calculations.
As I understand for "reverse perturbation" I assinged
the inintial charges to be zero on all ligand atoms
and perturbed into normal charges at lambda = 1. First
of all the energy remains positive in vacume after 500
NCYC and 1000 MAXCYC comparing to the normal case
(charged --> uncharged) whose energy drops quickly.
Therefore it is easy to understand why the following
md blows out.
For the similar calculation in water, I first
minimized the water with initial restraints on the
ligand. Then I assign the initial dummy atom types at
lambda = 0 and perturb into normal ones at the end.
However the dv/dl term remains zero throughout the
simulations.
Thank you for any suggestions.
Eric
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Received on Sat Feb 12 2005 - 02:53:00 PST
