VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 28 2017 - 16:28:07 CST

We would definitely need to see the error messages (if any) that VMD
emits when reading the file in order to say much about what might
be happening here. Best would be to provide us with a copy of
a file that you have trouble loading by posting it somewhere for download.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 25, 2017 at 02:10:53PM +1300, Ashar Malik wrote:
> Hey Sanim,
> Going with what you said you don't say what error do you get?Â
> Does the file load without errors and you dont see anything?
> If you are combining 3 structures (with simple cat and assuming there are
> no errors there with atom numbers) are they at the same point in space? If
> the three structures are too far in space and you load everything you will
> look at the centre which may not have anything I think.Â
> To check for this when you load a gro file and assuming there is no error
> the VMD main window should display the name of the file and the number of
> atoms and frames. Do those fields get populated?
> If yes then it's probably that the structures in the three files are
> spatially too far apart. Try loading the three individual structures
> seperately and see if they overlap.
> If you are getting an error maybe mention that. Otherwise try seeing where
> they are ... Otherwise write back and someone will help.
> Best of luck.
> /A
> On Feb 25, 2017 13:09, "Sanim Rahman" <[1]sanimr_at_mail.usf.edu> wrote:
>
> Hello all,
> I am having an issue viewing a .gro file I generated in GROMACS. I am
> aware of issues highlighted in past threads about the structure not
> showing up at all in VMD due to an " unexpected end-of-file reached"
> error. I fixed the number of atoms within the system to remove this
> error and I am still unsuccessful in viewing the structure. I also
> picked extreme dimensions for my system by multiplying each dimension by
> 100 and that still failed.
> The file was generated by combing three .gro files by using:
> cat file1.gro file2.gro file3.gro > file4.gro
> I have also tested the first three files and was able to view them
> individually in VMD. So the error must have occurred in combining the
> files. I will truly appreciate any assistance! Â Â
> Regards,
> Sanim Rahman
>
> References
>
> Visible links
> 1. mailto:sanimr_at_mail.usf.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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