Zhanglab forum

Dear Shijie, Thank you for using our software, we only test the program on A40, V100, and A100 GPU cards, and never tried RTX4090, so I am not sure I can help with this issue. But have you ever tried this ticket https://zhanggroup.org/forum/viewtopic.php?f=3&t=1010&sid=5e1ad01058db09c1807abd...

Dear user,

You can ignore this warning, this is may be you run the program two times, and the first time those links are created, the program should run without a problem when you see this message. Let us know if you have any other trouble.

Best Regards
Wei Zheng

Hi Zijian,

Yes, please change to another email address, some emails seem to have issues with receiving our notification email, we think it is an issue from your email server side, and can not be solved by our side. Thank you.

Best Regards
Wei Zheng

Dear Zijian,

We have sent the jobs to your email. and maybe next time you should change another email. Thank you.

Best Regards
Wei Zheng

Dear Zijian,

We didn't find you have jobs running on DMFold, you can test submit your job again.

BTW, try to clean your input sequence, despite we have implemented the non-ascii code dealing function, we suggest only containing the 'English word' in your input information.

Best Regards
Wei Zheng

Hi Xin-Dong,

Yes, sometimes the amber refinement has an issue with GPU, you can either use CPU to do refinement (it still has some change failed) or cancel it and use other tools to remove clash (if exists).

Glad to see you solve the problems.

Best
Wei

Hi Xin-Dong Based on the message I guess it may be the issue from Google Jax, You can try a different version Jax, if you used CUDA11, maybe pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 numpy==1.20.1 sci...

Dear Xin-Dong Xu, Thank you for using our software. First, you can ignore the 'Warning message, it is not the error'. Second, please make sure that you correctly run the ./Install_af2_env.sh command and the AlphaFold2 package is successfully installed in your cluster. You can try $DMFold_dir/bin/alp...

Dear Wenlong, What email did you use? Gmail? Gmail sometimes has issues getting our server email which may be due to Google email server issue for an unknown reason. I would suggest you change to another email next time. Let me know your email used for submitting, I will forward the job ID by person...

Dear Wenlong,

We have fixed the issue, and now you can submit it.

Best Regards
Wei Zheng