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GHeinzelmann / BAT.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
MIT License
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Free energy calculation step not finding files from equilibration step #32

Closed mixarcid closed 10 months ago

mixarcid commented 10 months ago

I'm trying to run the example calculation (I haven't changed input-dd.in). The equilibration step python BAT.py -i input-dd.in -s equil appeared to run successfully -- I've attached the full output below.

equil.txt

However, when I run the free energy step python BAT.py -i input-dd.in -s fe, I get the following error:

lambda values: [0.025446043828620757, 0.12923440720030277, 0.2970774243113014, 0.5, 0.7029225756886985, 0.8707655927996972, 0.9745539561713792]
Gaussian weights: [0.06474248308443532, 0.1398526957446383, 0.19091502525255916, 0.20897959183673448, 0.19091502525255916, 0.1398526957446383, 0.06474248308443532]
Setting up pose0
window: c00 weight: 0.0
Traceback (most recent call last):
  File "[...]/BAT/BAT.py", line 720, in <module>
    anch = build.build_dec(fwin, hmr, mol, pose, comp, win, water_model, ntpr, ntwr, ntwe, ntwx, cut, gamma_ln, barostat, receptor_ff, ligand_ff, dt, sdr_dist, dec_method, l1_x, l1_y, l1_z, l1_range, min_adis, max_adis, ion_def, other_mol, solv_shell)
  File "/home/boris/Repos/BAT.py/BAT/lib/build.py", line 440, in build_dec
    shutil.copy('../../../equil/'+pose+'/md%02d.rst7' %fwin, './')
  File "[...]/shutil.py", line 417, in copy
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "[...]/shutil.py", line 254, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '../../../equil/pose0/md08.rst7'

Any idea what's going on here? Thanks for your help!

mixarcid commented 10 months ago

Nvm -- I see this is a duplicate of https://github.com/GHeinzelmann/BAT.py/issues/24