Zhanglab forum

Hi Wei, I am very grateful for your insightful response. It turns out that the instability lies in the structure of this protein, and I mistakenly thought there was an issue with my installation. Thank you for all your help and I look forward to learning from you again. Wishing you all the best. Bes...

Hi Wei, I am writing to confirm whether you have received the files I shared with you via email. I attached the working directory of my DMFold run, which includes the model and multiple sequence alignment files. Kindly let me know if you have successfully received the files. Thank you once again for...

Hi Wei, I would like to express my sincere gratitude for your previous assistance, which enabled me to successfully install and run DMfold locally. However, upon comparing the structures obtained from my local run with those predicted by the online version of DMfold (https://seq2fun.dcmb.med.umich.e...

Hi Wei,

It seems to be a problem with AlphaFold2. Running with the option “–run_relax=false” could help resolve this error.

I found this solution on https://github.com/google-deepmind/alphafold/issues/466.

Best regards,
Xin-Dong

Dear Wei, I wanted to express my sincere gratitude for the advice you provided. It successfully resolved the error I encountered. However, while continuing the process, I encountered a new error message, "Traceback (most recent call last): File "/data/DMFold/bin/alphafold/run_alphafold_msa...

Dear Zheng Wei, Thank you for your previous suggestions, they were very helpful to me. After testing the multiple options you provided, it seems that there was an issue with my Conda environment configuration. I manually reconfigured the conda environment according to the Install_af2_env.sh script, ...

Dear Wei Zheng,

This is the sequence I am testing:

>DEFB
MKSLLFTLAVFMLLAQLVSGNWYVKKCLNDVGICKKKCKPEEMHVKNGWATCGKQRDCCVPADRRANYPVFCVQTRTTRISTV
It is an antimicrobial peptide with a length of 80 amino acids.

Best regards,

Xin-Dong Xu

Dear Wei Zheng,

Thank you for your valuable suggestions. I will reply to you as soon as possible after testing these options.

Best regards,

Xin-Dong Xu

After downloading the DMFold installation package from the provided link and following the instructions in the readme file to install it on our server, I encountered the following error during the testing phase: "WARNING! No such file: /data/DMFold/database/UniRef30_2022_02/UniRef30_2022_02.cs2...