-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error When Running AlphaPanda #1
Comments
Thanks for your attention. how about your input file?
胡岳
***@***.***
…---- Replied Message ----
From aaaaaaaaa21-code ***@***.***> Date 09/20/2024 16:31 To YueHuLab/AlphaPanda ***@***.***> Cc Subscribed ***@***.***> Subject [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1)
Hello,
I’m interested in using the model, but I’m encountering an error when I try to run it. During execution, the data seq heavy seqmap prints information like:
{('B', 1, ' '): 0, ('B', 2, ' '): 1, ('B', 3, ' '): 2, ..., ('B', 16, ' '): 15, ...}
After that, the program fails with the following error:
Sampling: 0%| | 0/100 [00:06<?, ?it/s]
antibody.pdb-H_CDR1: 0%| | 0/2 [00:06<?, ?it/s]
Traceback (most recent call last):
File "design_AlphaPanda.py", line 4, in
design_for_pdb(args_from_cmdline())
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/tools/runner/design_for_pdb.py", line 233, in design_for_pdb
traj_batch = model.sample(batch, sample_opt={
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/models/diffab.py", line 134, in sample
traj = self.diffusion.sample(v_0, p_0, s_0, res_feat, pair_feat, mask_generate, mask_res, batch, **sample_opt)
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 995, in sample
v_next, R_next, eps_p, c_denoised = self.eps_net(
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 692, in forward
res_feat2=res_feat.reshape(L, self.res_feat_dim)
RuntimeError: shape '[128, 128]' is invalid for input of size 98304
I would greatly appreciate any assistance in identifying the cause of this RuntimeError and guidance on how to fix it.
Thank you!
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
|
I input a PDB file of an antigen-antibody complex, where the B chain is the heavy chain of the antibody. I was able to successfully run Diffab with this PDB file. |
you may design antibody once a time. The software only support design one structure in one run. Have a try. The checkpoint is a toy one. when published, we would make a useful checkpoint public.
胡岳
***@***.***
…---- Replied Message ----
From aaaaaaaaa21-code ***@***.***> Date 09/20/2024 16:46 To YueHuLab/AlphaPanda ***@***.***> Cc Yue Hu ***@***.***>,
Comment ***@***.***> Subject Re: [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1)
Thanks for your attention. how about your input file? 胡岳 @.***
…
---- Replied Message ---- From aaaaaaaaa21-code @.> Date 09/20/2024 16:31 To YueHuLab/AlphaPanda @.> Cc Subscribed @.***> Subject [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1) Hello, I’m interested in using the model, but I’m encountering an error when I try to run it. During execution, the data seq heavy seqmap prints information like: {('B', 1, ' '): 0, ('B', 2, ' '): 1, ('B', 3, ' '): 2, ..., ('B', 16, ' '): 15, ...} After that, the program fails with the following error: Sampling: 0%| | 0/100 [00:06<?, ?it/s] antibody.pdb-H_CDR1: 0%| | 0/2 [00:06<?, ?it/s] Traceback (most recent call last): File "design_AlphaPanda.py", line 4, in design_for_pdb(args_from_cmdline()) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/tools/runner/design_for_pdb.py", line 233, in design_for_pdb traj_batch = model.sample(batch, sample_opt={ File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(*args, **kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/models/diffab.py", line 134, in sample traj = self.diffusion.sample(v_0, p_0, s_0, res_feat, pair_feat, mask_generate, mask_res, batch, **sample_opt) File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(*args, **kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 995, in sample v_next, R_next, eps_p, c_denoised = self.eps_net( File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl return forward_call(input, kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 692, in forward res_feat2=res_feat.reshape(L, self.res_feat_dim) RuntimeError: shape '[128, 128]' is invalid for input of size 98304 I would greatly appreciate any assistance in identifying the cause of this RuntimeError and guidance on how to fix it. Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.>
I input a PDB file of an antigen-antibody complex, where the B chain is the heavy chain of the antibody. I was able to successfully run Diffab with this PDB file.
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you commented.Message ID: ***@***.***>
|
Thank you for your response. I tried modifying the input to include only the antibody's PDB, but the same error still occurs. I look forward to your new checkpoints. |
Thanks. It not the only antibody pdb,but the complex pdb. Change the *.yml file, to design 1 structure in a run.
胡岳
***@***.***
…---- Replied Message ----
From aaaaaaaaa21-code ***@***.***> Date 09/20/2024 16:58 To YueHuLab/AlphaPanda ***@***.***> Cc Yue Hu ***@***.***>,
Comment ***@***.***> Subject Re: [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1)
you may design antibody once a time. The software only support design one structure in one run. Have a try. The checkpoint is a toy one. when published, we would make a useful checkpoint public. 胡岳 @.***
…
---- Replied Message ---- From aaaaaaaaa21-code @.> Date 09/20/2024 16:46 To YueHuLab/AlphaPanda @.> Cc Yue Hu @.>, Comment @.> Subject Re: [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1) Thanks for your attention. how about your input file? 胡岳 @.*** … ---- Replied Message ---- From aaaaaaaaa21-code @.> Date 09/20/2024 16:31 To YueHuLab/AlphaPanda @.> Cc Subscribed @.***> Subject [YueHuLab/AlphaPanda] Error When Running AlphaPanda (Issue #1) Hello, I’m interested in using the model, but I’m encountering an error when I try to run it. During execution, the data seq heavy seqmap prints information like: {('B', 1, ' '): 0, ('B', 2, ' '): 1, ('B', 3, ' '): 2, ..., ('B', 16, ' '): 15, ...} After that, the program fails with the following error: Sampling: 0%| | 0/100 [00:06<?, ?it/s] antibody.pdb-H_CDR1: 0%| | 0/2 [00:06<?, ?it/s] Traceback (most recent call last): File "design_AlphaPanda.py", line 4, in design_for_pdb(args_from_cmdline()) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/tools/runner/design_for_pdb.py", line 233, in design_for_pdb traj_batch = model.sample(batch, sample_opt={ File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(*args, **kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/models/diffab.py", line 134, in sample traj = self.diffusion.sample(v_0, p_0, s_0, res_feat, pair_feat, mask_generate, mask_res, batch, **sample_opt) File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(args, kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 995, in sample v_next, R_next, eps_p, c_denoised = self.eps_net( File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl return forward_call(input, kwargs) File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 692, in forward res_feat2=res_feat.reshape(L, self.res_feat_dim) RuntimeError: shape '[128, 128]' is invalid for input of size 98304 I would greatly appreciate any assistance in identifying the cause of this RuntimeError and guidance on how to fix it. Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.> I input a PDB file of an antigen-antibody complex, where the B chain is the heavy chain of the antibody. I was able to successfully run Diffab with this PDB file. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>
Thank you for your response. I tried modifying the input to include only the antibody's PDB, but the same error still occurs. I look forward to your new checkpoints.
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you commented.Message ID: ***@***.***>
|
Thank you for your help! After changing the design quantity to 1, it successfully ran. |
Hello,
I’m interested in using the model, but I’m encountering an error when I try to run it. During execution, the data seq heavy seqmap prints information like:
{('B', 1, ' '): 0, ('B', 2, ' '): 1, ('B', 3, ' '): 2, ..., ('B', 16, ' '): 15, ...}
After that, the program fails with the following error:
Sampling: 0%| | 0/100 [00:06<?, ?it/s]
antibody.pdb-H_CDR1: 0%| | 0/2 [00:06<?, ?it/s]
Traceback (most recent call last):
File "design_AlphaPanda.py", line 4, in
design_for_pdb(args_from_cmdline())
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/tools/runner/design_for_pdb.py", line 233, in design_for_pdb
traj_batch = model.sample(batch, sample_opt={
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/models/diffab.py", line 134, in sample
traj = self.diffusion.sample(v_0, p_0, s_0, res_feat, pair_feat, mask_generate, mask_res, batch, **sample_opt)
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 995, in sample
v_next, R_next, eps_p, c_denoised = self.eps_net(
File "/media/dell/newdisk/mambaforge/envs/AlphaPanda/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/media/dell/newdisk/AlphaPanda-main/AlphaPanda/modules/diffusion/dpm_full.py", line 692, in forward
res_feat2=res_feat.reshape(L, self.res_feat_dim)
RuntimeError: shape '[128, 128]' is invalid for input of size 98304
I would greatly appreciate any assistance in identifying the cause of this RuntimeError and guidance on how to fix it.
Thank you!
The text was updated successfully, but these errors were encountered: