IndexError: list index out of range

[pablo-arantes]

Hi flamel team,

Thank you for your work on flamel, it's a great tool. We are trying to use for our system, and we are getting the following issue:

Traceback (most recent call last):
File "/home/aakash/anaconda3/envs/afe/bin/flamel", line 8, in
sys.exit(main())
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/flamel/flamel.py", line 109, in main
workflow.run(skiptime=args.equiltime, uncorr=args.uncorr,
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 235, in run
self.read(use_FEP, use_TI)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 144, in read
column_names = u_nk_list[0].columns.values.tolist()
IndexError: list index out of range

Following the command line that we are using to run the alchemical free energy calculations:

flamel -a AMBER -p mdnvt_prod_ -f 10 -g -j result.csv -m MBAR -n dE -o out_data -q csv -r 3 -s 0 -t 298 -v -w

Can you, please, help us in this issue?

Thank you.

Best,

Pablo

[xiki-tempula]

Many thanks for the issue. I wonder if I could have the input file so I could have a test? Thanks.
By the way, why is the amber file suffix -q csv? I thought that the amber output file is out?

[pablo-arantes]

Hi,

Thank you for your reply. Follow the file we are using.

Thank you.
mdnvt_prod_1.out.zip

[xiki-tempula]

Ok, It would run if you change -q csv to -q out as the extension of your file is out, you would also need to change -t 298 to -t 300 as it is 300K.

[pablo-arantes]

Hi, I've changed everything as you suggested and I'm having the following issue:

**11962 MBAR energies are > 0.0 kcal/mol
Error reading u_nk from ./mdnvt_prod_8.out.
Traceback (most recent call last):
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 121, in read
u_nk = self._extract_u_nk(file, T=self.T)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/parsing/amber.py", line 419, in extract_u_nk
extracted = extract(outfile, T)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/parsing/init.py", line 27, in wrapper
dict_with_df = func(outfile, T, *args, **kwargs)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/parsing/amber.py", line 347, in extract
mbar_time = [
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/parsing/amber.py", line 348, in
file_datum.t0 + (frame_index + 1) * file_datum.dt * file_datum.ntpr
TypeError: unsupported operand type(s) for +: 'NoneType' and 'float'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/aakash/anaconda3/envs/afe/bin/flamel", line 8, in
sys.exit(main())
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/flamel/flamel.py", line 109, in main
workflow.run(skiptime=args.equiltime, uncorr=args.uncorr,
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 235, in run
self.read(use_FEP, use_TI)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 128, in read
raise OSError(msg) from exc
OSError: Error reading u_nk from ./mdnvt_prod_8.out.**

Thank you again.

[xiki-tempula]

Interesting, I wonder if I can have this file mdnvt_prod_8.out? Thanks.

[pablo-arantes]

Sure. Follow the file. Thank you!
mdnvt_prod_8.out.zip

[xiki-tempula]

@pablo-arantes Thanks. Do you mind pull the latest version of alchemlyb? I think it should be fixed now.

[pablo-arantes]

Hi,

Thank you so much for the help. I've installed the last version of alchemlyb and now I'm getting the following issue:

11962 MBAR energies are > 0.0 kcal/mol
5923 MBAR energies are > 0.0 kcal/mol
11971 MBAR energies are > 0.0 kcal/mol
11968 MBAR energies are > 0.0 kcal/mol
11967 MBAR energies are > 0.0 kcal/mol
2642 MBAR energies are > 0.0 kcal/mol
4967 MBAR energies are > 0.0 kcal/mol
/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/scipy/optimize/_minimize.py:555: RuntimeWarning: Method BFGS does not use Hessian information (hess).
MBAR weights converged within tolerance, despite the SciPy Warnings. Please validate your results.
Traceback (most recent call last):
File "/home/aakash/anaconda3/envs/afe/bin/flamel", line 8, in
sys.exit(main())
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/flamel/flamel.py", line 109, in main
workflow.run(skiptime=args.equiltime, uncorr=args.uncorr,
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 269, in run
ax = self.plot_overlap_matrix(overlap)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/alchemlyb/workflows/abfe.py", line 626, in plot_overlap_matrix
ax.figure.savefig(join(self.out, overlap))
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/figure.py", line 3274, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 2338, in print_figure
result = print_method(
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 2204, in
print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/backends/backend_pdf.py", line 2808, in print_pdf
file = PdfFile(filename, metadata=metadata)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/backends/backend_pdf.py", line 713, in init
fh, opened = cbook.to_filehandle(filename, "wb", return_opened=True)
File "/home/aakash/anaconda3/envs/afe/lib/python3.9/site-packages/matplotlib/cbook/init.py", line 492, in to_filehandle
fh = open(fname, flag, encoding=encoding)
FileNotFoundError: [Errno 2] No such file or directory: 'out_data/O_MBAR.pdf'

Thank you.

[xiki-tempula]

Ok, I think it just means that the folder out_data doesn't exist. I will make a fix. In the mean time, if you create the folder yourself, I think it would run.

[xiki-tempula]

I think all of the problems has been fixed in this issue.