[gmx-users] Trouble getting gmx gyrate to work (Windows/Ubuntu)

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 23:21:18 CET 2019

On 2/4/19 4:30 PM, Ben Drewry wrote:
> I just downloaded gromacs to do radius of gyration calculations on a
> theoretical molecule, and its not recognizing the file ive downloaded to
> analyze.
> I'm running the Microsoft Store app for Ubuntu on Windows, I've succesfully
> installed gromacs for use with the app, and have the file as a .pdb
> extension. When i try using "gmx gyrate -f [filename.pdb]" with the full
> path for the file, gromacs returns the error for invalid command line
> options, saying the file does not exist or is inaccessible. Even though it
> has full read-write-execute permissions.
> Does anyone have any insight on how to clear up these errors?

Please provide the full command and screen output, copied and pasted.

If you're actually enclosing the file name in brackets, that's incorrect.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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