DCD file does not exist

[pablo-arantes]

DCD file does not exist

[pablo-arantes]

Hi @dag2225,

Sorry for my delay.
Regarding your issue, it seems to me that your pathway or your job name is not the same that you have used to run. I mean, in the "Concatenate and align the trajectory" cell (image attached) you have the option to put your Google Drive Path (where you have your dcd files) and your Jobname (should be the same that you have used to run your production step).
For example, if you used 1AKI_prod as a Jobname in the production step, you should keep the same name for the concatenation step.

I hope it helps. Please, let me know if you have any question.

Thank you.

Best,

Pablo

[dag2225]

Hi Pablo, thanks for the helpful information! I tried this with all the default filled in values relating to 1AKI, but unfortunately it did not fix my problem. I did also check, and I have a file in /content/drive/MyDrive called "1aki_prod_1.dcd". Since this file exists, and I checked that the jobname for the production step and concatenation step match, I am again not sure how to fix the problem.

At the end of the "Runs a Production MD Simulation" cell, I get the output:

Writing state file (/content/drive/MyDrive/1aki_prod_1.rst)...
Writing coordinate file (/content/drive/MyDrive/1aki_prod_1.pdb, frame = 200)...
Finished!

with all the default filled in values kept the same as when I first opened the Colab link. Attached are screenshots of the files the code I have been able to run from the notebook has generated in my drive. Hope this additional information is helpful, and we can figure out what is wrong - I appreciate your patience, as I am very new to protein MD simulation :)

[pablo-arantes]

Hi @dag2225,

Thank you for your feedback. Regarding your error, I think I got it what is the issue. You have only one dcd file in your folder, in other words, you have used only 1 stride in the production options. You should keep the same options in the Concatenate and align the trajectory cell. Follow the picture where I tried, and it worked well for me.

Probably, you are using Number_of_strides = 2 in this cell, however you only have 1 stride (one dcd file in your folder). I've done a test with Number_of_strides = 2, and I had the same error. Please use Number_of_strides = 1.

One tip, when you are going to run and save the files on your Google Drive, please, create a folder in your Drive and save there. I think it is going to help to find and organize all the files created during the simulations.

I hope it helps. Please, let me know if you have any questions.

Thank you.

Best,

Pablo

[dag2225]

Hi Pablo, that appears to have solved the problem. Thank you so much for your continued help!! I am excited to continue exploring how your notebook can be used for my research :)