DCD file not loading to MDAnalysis

[Devanshi Pandya]

Hello!

When I run the following:

u = MDAnalysis.Universe(psf, dcd)

where psf and dcd are my own topology and trajectory files loaded and from my computer and opened, I get the error:

'_io.TextIOWrapper' object has no attribute 'encode'

Here is a OneDrive link to the dcd file.

https://prodduke-my.sharepoint.com/:u:/g/personal/dp243_duke_edu/EXlgbdCiTqVOhARDjcWz4Y8ByE6RV720OyoqIcXWIJHaxg

This error doesn't arise when I make a universe with just the psf file, is there anything I need to do in order to make the dcd file compatible?

Thanks,

Devanshi

[Oliver Beckstein]

Hi Devanshi,

Welcome to the MDAnalysis mailing list!

Can you please tell us

- your operating system

- version of Python

- version of MDAnalysis

- how you installed MDAnalysis

That might help us to get a better idea.

Please copy and paste the *whole* output of the error in the email.

Thanks,

Oliver

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[Devanshi Pandya]

Linux OS, Python 3.6, used conda to install the latest version of MDAnalysis.

Here is the entire error message:

Thanks so much!

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Devanshi Pandya

Duke Rhydhun Executive Captain

Duke-UNICEF Student Advisory Counselor

[Oliver Beckstein]

Hi Devanshi,

What exactly is “dcd”? Please provide the code that defines this variable.

Oliver

On Nov 2, 2021, at 11:05 AM, Devanshi Pandya <devan...@gmail.com> wrote:

Linux OS, Python 3.6, used conda to install the latest version of MDAnalysis.

Here is the entire error message:

<image.png>

Thanks so much!

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CA%2BbHQ8rC_47kOKBbUW9XdXzBJG0fBh0cm2WBk4d1WZ_XT%3DU4hA%40mail.gmail.com.

[Devanshi Pandya]

This is the line:

dcd = open("5ibo22T370.dcd")

Where the file being opened is the dcd file I sent the OneDrive link to earlier. The psf file was opened similarly:

psf = open("5ibo22k.psf") and gave no errors if I make a universe of just psf, which is why I believe the error has something to do with the dcd file.

Thanks,

Devanshi

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/F08B23E9-C2D8-4116-BE69-383A3B6C2BEC%40gmail.com.

[Irfan Alibay]

Hi Devanshi,

MDAnalysis expects the path of the file for inputs, not a file object.

Please try just doing:

u = mda.Universe("5bio22k.psf", "5bio22T370.dcd")

Best regards,

Irfan