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Errors with RMSD pcoord

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shelby santos

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Sep 18, 2024, 12:39:29 PM9/18/24
to westpa-users
Hello, 

I am running into errors with getting set up and using WESTPA for my rmsd-pcoord run. If I had to guess, I think there is some issue with pcoord.py recognizing my reference file for the RMSD calculation, and I'm still learning how all the different files connect. I have included the error message along with the seg_log and pcoord.py file in the attachments. If anyone has any ideas or suggestions on how to troubleshoot this error, it would be greatly appreciated! Thanks!

Best, 
Shelby Santos
pcoord.py
slurm-42003695.out
000001-000001.log

Jeremy Leung

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Sep 18, 2024, 12:46:24 PM9/18/24
to westpa-users
Hi Shelby!

You're passing a string as the reference file. You need to open it as a mda.Universe object and pass it to the function.

So replace the last two lines of your pcoord.py with something like this:
```
u_3BRI = mda.Universe(args.top_file, args.traj_file) 
u_ref = mda.Universe(args.top_file, args.ref_file)
rmsd_dim(args.top_file, u_3BRI, u_ref)
```

Best,

Jeremy L.
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