DCD file not loading to MDAnalysis

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Devanshi Pandya

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Oct 21, 2021, 1:28:51 PM10/21/21
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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

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Oct 21, 2021, 1:31:28 PM10/21/21
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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

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Nov 2, 2021, 2:06:18 PM11/2/21
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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!

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Devanshi Pandya
Duke Rhydhun Executive Captain
Duke-UNICEF Student Advisory Counselor

Oliver Beckstein

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Nov 2, 2021, 8:09:23 PM11/2/21
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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!

Devanshi Pandya

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Nov 5, 2021, 10:55:13 AM11/5/21
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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

Irfan Alibay

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Nov 5, 2021, 11:00:53 AM11/5/21
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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
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