I successfully executed the preprocess and sampling code using the example file (3g8i). However, when I attempted to use the same code with my input file, I encountered an error. Could you please help me identify the issue? I've attached my input file for your reference.
(dragonfly_gen) hp@hp:~/Downloads/dragonfly_gen/genfromstructure$ python preprocesspdb.py -pdb_file 1ZUA_protein -mol_file 1ZUA_ligand -pdb_key 1ZUA
Number of embedded atoms: 257 / 156
Writing input/1ZUA.h5
(dragonfly_gen) hp@hp:~/Downloads/dragonfly_gen/genfromstructure$ python sampling.py -config 901 -epoch 194 -T 0.5 -pdb 1ZUA -num_mols 100
Sampling 100 molecules:
0%| | 0/100 [00:00<?, ?it/s]
Traceback (most recent call last):
File "sampling.py", line 233, in
novels, probs_abs = temperature_sampling(
File "sampling.py", line 100, in temperature_sampling
hiddens = egnn(g)
File "/home/hp/anaconda3/envs/dragonfly_gen/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/home/hp/Downloads/dragonfly_gen/genfromstructure/net.py", line 178, in forward
torch.cat(
RuntimeError: Sizes of tensors must match except in dimension 1. Expected size 257 but got size 156 for tensor number 1 in the list.
Hello Dragonfly Gen Team,
Thank you for creating such an impressive tool.
I successfully executed the preprocess and sampling code using the example file (3g8i). However, when I attempted to use the same code with my input file, I encountered an error. Could you please help me identify the issue? I've attached my input file for your reference.
Thank you for your assistance.
1ZUA.zip
(dragonfly_gen) hp@hp:~/Downloads/dragonfly_gen/genfromstructure$ python preprocesspdb.py -pdb_file 1ZUA_protein -mol_file 1ZUA_ligand -pdb_key 1ZUA Number of embedded atoms: 257 / 156 Writing input/1ZUA.h5
(dragonfly_gen) hp@hp:~/Downloads/dragonfly_gen/genfromstructure$ python sampling.py -config 901 -epoch 194 -T 0.5 -pdb 1ZUA -num_mols 100 Sampling 100 molecules: 0%| | 0/100 [00:00<?, ?it/s] Traceback (most recent call last): File "sampling.py", line 233, in
novels, probs_abs = temperature_sampling(
File "sampling.py", line 100, in temperature_sampling
hiddens = egnn(g)
File "/home/hp/anaconda3/envs/dragonfly_gen/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/home/hp/Downloads/dragonfly_gen/genfromstructure/net.py", line 178, in forward
torch.cat(
RuntimeError: Sizes of tensors must match except in dimension 1. Expected size 257 but got size 156 for tensor number 1 in the list.