VMD-L Mailing List

From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Tue Jun 17 2008 - 13:51:36 CDT

jake wernik wrote:
> I am trying to open a gromacs .gro file with my atomic coordinates but
> VMD gives the following message upon opening and does not display the
> molecule, only lists the number of atoms without bonds:
>
> Info) Using plugin gro for structure file E:/file.gro
> *Warning, error reading box, unexpected end-of-file reached*
> Info) Using plugin gro for coordinates from file E:/file.gro.
> Info) Finished with coordinate file E:/file.gro
> Info) Analyzing structure ...
> Info) etc....
When that kind of things happens to me, it is generally because the
number of atoms specified on the second line of the gro file is
different from the number of atoms really present in the file. Check
also that the box is correctly described at the last line of your file.

Hope that helps

Nicolas
>
> Can someone help explain what is wrong with the file format as I have
> loaded a similar .gro file before and it worked just fine. It seems
> that the program is very picky with the amount of characters or spaces
> used to define the parameters in the file.
>
> Also, is there any resource available where I can read up on what the
> warning messages mean?
>
> Thanks in advance.
>
> Mr. Wernik