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

[Ben Drewry]

I figured out that, removed the brackets and we were able to move forward
on the calculations. The issue is (am undergrad working under PhD student)
is that we want to calculate radius of gyration of a "theoretical" 3 atom
molecule. That is, we are defining three arbitrary atoms that aren't actual
elements. We ended up getting an error that it couldn't fetch the mass for
the atom, since it's just a "theoretical" atom that doesn't exist in real
life.

Is there any way we can pass arbitrary information to the gromacs database
to allow for the RG calculation for this "theoretical" molecule?

Ben

On Mon, Feb 4, 2019 at 4:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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