index 50 is out of bounds

[aspitaleri]

Hi
I am trying to use convert_dataset.py on my simulation. I converted the xtc to pdb containing only CA, having 100,001 MODEL. The number of residues are 489 and I run as follow:

python convert_dataset.py --MDfolder data/pdb/ --num-residues 489
I tried also
python convert_dataset.py --MDfolder data/pdb/ --pdb-start 1 --num-residues 489 --train-interval 2000 --validate-interval 2000

but I get:

Generate Train
Start: 1th PDB
Traceback (most recent call last):
File "convert_dataset.py", line 344, in
features, edges = convert_dataset_md_single(MDfolder, startIndex=1, experiment_size=1, timestep_size=50,
File "convert_dataset.py", line 304, in convert_dataset_md_single
features.append(read_feature_MD_file_slidingwindow(MDfolder+"ca_"+str(
File "convert_dataset.py", line 129, in read_feature_MD_file_slidingwindow
feature[numStep, 0, int(words[4])-aa_start] = float(words[5])
IndexError: index 50 is out of bounds for axis 0 with size 50

From the code I could not see where the error is from.
The demo ca_1.pdb worked fine. I am using 1 GPU A100 and 60G of memory
Any help to understand the options requirement?

[Peter-obi]

Did you find any solution to this?

[aspitaleri]

Yes -
I add --test-interval 2001 too. Basically 100,001/50 ~ 2001

[Peter-obi]

Thanks!