Dear amber users,
I'm running LIE analysis using the FEW in amber 16. I'm able to run it successfully on most of the selected small molecules.
I have tris as one of the small molecules. The calculation seems to be failing for this, it is not able to calculate the elec and vdw contributions for tris (Result file is shown below). I tried running the analysis using 1/many frames, still have the same problem. Did anyone encounter the same issue? Is there any parameter I can tweak to adjust the run for small molecules of the size of tris?
Looking forward to suggestions.
Thanks in advance.
Regards
Sowmya
Energy contributions:
Mean energy Standard deviation Standard error
Complex non-bonded VDW: -0.313538 4.479343 0.445711
Complex non-bonded ELE: -137.436829 36.240642 3.606079
SASA of bound ligand: 278.953871 41.252660 4.104793
Ligand non-bonded VDW: nan nan nan
Ligand non-bonded ELE: -inf nan nan
SASA of unbound ligand: 332.548053 43.685825 4.346902
================================================================================
Final LIE results:
Differences in interaction energies and SASA:
Delta electrostatic energy (dE-ele): inf kcal/mol
Delta van der Waals energy (dE-vdW): nan kcal/mol
SASA difference (dSASA): -53.594182 Å^^2
________________________________________________________________________________
Estimated binding free energy:
ATTENTION: Please note that the estimate of the binding free energy (dG-bind)
provided below was calculated according to the equation
dG-bind = alpha * dE-vdW + beta * dE-ele
with fixed coefficients of alpha=0.16 and beta=0.5.
We strongly recommend to thoroughly investigate whether using other
coefficients could be beneficial in the specific case.
Binding energy estimate (dG-bind): nan kcal/mol
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Received on Thu Mar 21 2019 - 07:00:02 PDT
