Hello All,
I'm using edgembar to calculate the relative binding free energy of two ligands to a protein receptor. When generating py from xml file using edgembar, there are inf in the generated py script. As such, python .py failed. Then I manually removed some positive energy values in the ti001.out file, the same error message occurs. Does anybody encounter the same issue? Is this related to the energy outliers in my output files?
This is how I did.
1) I followed the amber tutorial 7.1 ti using softcore potential. I used Amber 2024 pmemd.cuda to run ti simulation with modified ti-related parameters,
scbeta = 1.0,
gti_add_sc = 5
gti_scale_beta = 1
gti_ele_sc = 1
gti_vdw_sc = 1
gti_cut_sc = 2
gti_vdw_exp = 2
2) edgembar-amber2dats.py -o t1/dats ti001.out
3) xml can be successfully generated by DiscoverEdges.py
4) but when running time edgembar --halves --fwdrev ${xml}, i encountered errors, containing inf in .py file. I attached my py file.
By the way, the example cdk2 works well for me.
Additionally, I found some positive Mbar energies at some lambda windows, does anyone know if my current parameter (scbeta and those gti parameters) can be modified to get better results?
Thank you for any comments.
Regards,
Tongtong
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Received on Sun Dec 08 2024 - 20:00:03 PST
