AMBER Archive (2006)

Subject: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7

From: Pan, Yongmei (
Date: Thu May 11 2006 - 13:50:36 CDT

Hi, David and guys:
I use gibbs, amber7 to calculate free energy change from PHE to ALA in a 500 residue protein.For the ten different trajectories extracted from a stable MD simulation (rms difference <1.5), the perturbation energy varies from 4kcal/mol to 8kcal/mol. So why the perturbation from PHE to ALA is so unstable, and it seem that the result depends heavily on the starting structure. this case contrasts with those of SER to ALA, or ALA to GLY perturbation, which are much more stable among trajectories.
The second question is, why the perturbation for SER to ALA always fail, due to the shake failure? I also tried "electric decoupling", but the result was not good.
The way my perturbation is: The direction is from big group to small one, with diminishing atoms replaced by dummy atom. All the bond and angel parameters involving dummy atoms keep the same during the perturbation, while the mass, charge and non-bond parameters are set to zero for the dummy atoms.
I appreciate if anybody can give me advice.
Yongmei Pan
College of Pharmacy, University of Kentucky
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