Hi AMBER Users,
I am new to MMPB/GBSA calculations and am studying the binding of toluene,
fumaric Acid and benzylsuccinate to an enzyme. I was able to get the
implementation to work successfully for my system. I have some questions
regarding the analysis.
I have been able to calculate the overall binding energies using MMGBSA,
MMPBSA and decompose the binding energies among the key residues at the
active site.
I have the following questions with regards to analyzing the results
1. I find that the total binding free energies calculated from MMGBSA give
negative free energies of binding while the MMPBSA binding energies are
positive (~1 kcal/mol). Why would the MMPBSA free energies show
unfavourable binding while MMGBSA show favourable? The MMGBSA and MMPBSA
energies also do not display the same trend for my ligands.
2. I understand that the ligand also has to be mentioned in the print_res
specification for decomposition. In the output, (delta's total energy
section) the ligand contribution to the binding energy is also reported. I
am finding it difficult to understand how the ligand's binding energy be
decomposed onto itself?
3. I find that the majority (~90%) of the binding energy (deltas of the
total energies in the output) for the toluene binding is attributed to the
ligand itself. [Meaning that the B.E remains undecomposed]. What could I be
doing wrong? or is this due to the hydrophobic interactions stabilizing
toluene? In the case of fumaric acid the ligand contribution was ~20% only.
These were calculated from 20ns trajectories of the substrate bound
simulations with the substrate stable at the active site.
I will be grateful to any comments/guidance on how I can better understand
or improve my results.
Thank you.
--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Wed Feb 27 2013 - 17:00:03 PST
