Hello！
I followed the steps and used conda to run the code. At step 4, an error message was reported:
/root/BindCraft-main/functions/DAlphaBall.gcc: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory
WARNING!! DALPHABALL output nan at index 18446744073709551488
DALPHABALL output indicies not matching! 1!=18446744073709551488
ERROR:: Exit from: /home/benchmark/rosetta/source/src/core/scoring/packing/surf_vol.cc line: 164
Traceback (most recent call last):
File "/root/BindCraft-main/./bindcraft.py", line 141, in
trajectory_interface_scores, trajectory_interface_AA, trajectory_interface_residues = score_interface(trajectory_relaxed, binder_chain)
File "/root/BindCraft-main/functions/pyrosetta_utils.py", line 75, in score_interface
interface_delta_unsat_hbonds = buns_filter.report_sm(pose)
RuntimeError:
File: /home/benchmark/rosetta/source/src/core/scoring/packing/surf_vol.cc:164
[ ERROR ] UtilityExitException
ERROR:
What's more, when I re-run it a second time,it seems an module error
python -u ./bindcraft.py --settings './settings_target/PDL1.json' --filters './settings_filters/default_filters.json' --advanced './settings_advanced/default_4stage_multimer.json'
an error message was reported:
Running binder design for target PDL1
Design settings used: default_4stage_multimer
Filtering designs based on default_filters
Starting trajectory: PDL1_l114_s259588
WARNING: 'model_1_multimer_v3' not found
WARNING: 'model_2_multimer_v3' not found
WARNING: 'model_3_multimer_v3' not found
WARNING: 'model_4_multimer_v3' not found
WARNING: 'model_5_multimer_v3' not found
Stage 1: Test Logits
Traceback (most recent call last):
File "/root/BindCraft-main/./bindcraft.py", line 109, in
trajectory = binder_hallucination(design_name, target_settings["starting_pdb"], target_settings["chains"],
File "/root/BindCraft-main/functions/colabdesign_utils.py", line 97, in binder_hallucination
af_model.design_logits(iters=50, e_soft=0.9, models=design_models, num_models=1, sample_models=advanced_settings["sample_models"], save_best=True)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 354, in design_logits
self.design(iters, **kwargs)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 348, in design
self.step(lr_scale=lr_scale, num_recycles=num_recycles,
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 214, in step
self.run(num_recycles=num_recycles, num_models=num_models, sample_models=sample_models,
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 89, in run
model_nums = self._get_model_nums(num_models, sample_models, models)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 71, in _get_model_nums
ns = [ns[n if isinstance(n,int) else ns_name.index(n)] for n in models]
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 71, in
ns = [ns[n if isinstance(n,int) else ns_name.index(n)] for n in models]
IndexError: list index out of range
Hello！
I followed the steps and used conda to run the code. At step 4, an error message was reported:
/root/BindCraft-main/functions/DAlphaBall.gcc: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory
WARNING!! DALPHABALL output nan at index 18446744073709551488
DALPHABALL output indicies not matching! 1!=18446744073709551488
ERROR:: Exit from: /home/benchmark/rosetta/source/src/core/scoring/packing/surf_vol.cc line: 164
Traceback (most recent call last):
File "/root/BindCraft-main/./bindcraft.py", line 141, in
trajectory_interface_scores, trajectory_interface_AA, trajectory_interface_residues = score_interface(trajectory_relaxed, binder_chain)
File "/root/BindCraft-main/functions/pyrosetta_utils.py", line 75, in score_interface
interface_delta_unsat_hbonds = buns_filter.report_sm(pose)
RuntimeError:
File: /home/benchmark/rosetta/source/src/core/scoring/packing/surf_vol.cc:164
[ ERROR ] UtilityExitException
ERROR:
What's more, when I re-run it a second time,it seems an module error
python -u ./bindcraft.py --settings './settings_target/PDL1.json' --filters './settings_filters/default_filters.json' --advanced './settings_advanced/default_4stage_multimer.json'
an error message was reported:
Running binder design for target PDL1
Design settings used: default_4stage_multimer
Filtering designs based on default_filters
Starting trajectory: PDL1_l114_s259588
WARNING: 'model_1_multimer_v3' not found
WARNING: 'model_2_multimer_v3' not found
WARNING: 'model_3_multimer_v3' not found
WARNING: 'model_4_multimer_v3' not found
WARNING: 'model_5_multimer_v3' not found
Stage 1: Test Logits
Traceback (most recent call last):
File "/root/BindCraft-main/./bindcraft.py", line 109, in
trajectory = binder_hallucination(design_name, target_settings["starting_pdb"], target_settings["chains"],
File "/root/BindCraft-main/functions/colabdesign_utils.py", line 97, in binder_hallucination
af_model.design_logits(iters=50, e_soft=0.9, models=design_models, num_models=1, sample_models=advanced_settings["sample_models"], save_best=True)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 354, in design_logits
self.design(iters, **kwargs)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 348, in design
self.step(lr_scale=lr_scale, num_recycles=num_recycles,
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 214, in step
self.run(num_recycles=num_recycles, num_models=num_models, sample_models=sample_models,
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 89, in run
model_nums = self._get_model_nums(num_models, sample_models, models)
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 71, in _get_model_nums
ns = [ns[n if isinstance(n,int) else ns_name.index(n)] for n in models]
File "/home/node/anaconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 71, in
ns = [ns[n if isinstance(n,int) else ns_name.index(n)] for n in models]
IndexError: list index out of range