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

[Justin Lemkul]

On 2/5/19 11:55 AM, Ben Drewry wrote:
> 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?

The simplest approach is to write a topology and use the resulting .tpr 
file as input to gmx gyrate. For a 3-atom system, you can write the 
topology by hand in no time.

-Justin

> 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
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================