# Fatal error: Something is wrong in the coordinate formatting of file complex.gro **URL:** \ **Category:** User discussions\ **Created:** [March 18, 2021, 6:09pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777 "2021-03-18T18:09:05Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Richwell](https://avatars.discourse-cdn.com/v4/letter/r/779978/32.png) [@Richwell](https://gromacs.bioexcel.eu/u/Richwell)\ **Post date:** [March 18, 2021, 6:09pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/1 "2021-03-18T18:09:05Z")
GROMACS version: 5.1.1 GROMACS modification: Yes/No Hello. I am working on protein-ligand MD, but I am facing difficulties in making the complex.gro. I initially made the mistake of not increasing my atom count on the second line of my complex.gro file, so I got the bad box warning. I then made the necessary corrections and included the additional ligand atoms to the count. I am now getting this error: Fatal error: Something is wrong in the coordinate formatting of file 1bkn5b.gro. Note that gro is fixed format (see the manual) For more information and tips for troubleshooting, please check the GROMACS website at [http://www.gromacs.org/Documentation/Errors](https://www.researchgate.net/deref/http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors) My complex.gro file looks like this: Gyas ROwers Mature At Cryogenic Speed 5456 20VAL N 1 9.505 6.917 8.459 20VAL H1 2 9.524 6.917 8.361 . . . 1FB5b H 46 25.715 21.334 -0.014 1FB5b H 47 25.908 21.451 0.104 1FB5b H 48 26.224 20.779 -0.018 8.13590 9.16000 6.11230 ---
**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\ **Post date:** [March 19, 2021, 10:18am UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/2 "2021-03-19T10:18:13Z")
Hello, the error message concerns [the file formatting](https://manual.gromacs.org/current/reference-manual/file-formats.html#gro), which is impossible to see in your posted message since that removes the formatting. Could you upload the file somewhere, or post the snippet inside a code block? Regards, Petter ---
**Author:** ![miki](https://avatars.discourse-cdn.com/v4/letter/m/df788c/32.png) [@miki](https://gromacs.bioexcel.eu/u/miki)\ **Post date:** [September 23, 2024, 10:10am UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/3 "2024-09-23T10:10:31Z")
Hi, pls how did your eventual solve this problem: Fatal error: Something is wrong in the coordinate formatting of file complex.gro. Note that gro is fixed format (see the manual) I’m facing the same problem ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 23, 2024, 10:22am UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/4 "2024-09-23T10:22:00Z")
Hi, It’s very difficult to help you without access to the file. Would you be able to post it somewhere? ---
**Author:** ![miki](https://avatars.discourse-cdn.com/v4/letter/m/df788c/32.png) [@miki](https://gromacs.bioexcel.eu/u/miki)\ **Post date:** [September 23, 2024, 10:42am UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/5 "2024-09-23T10:42:51Z")
Hi, Thanks for getting back to me. I can share the file. Please find them attached. Thanks. Chukwiuemeka Okolo (Attachment complex.gro is missing) > **(attachments)** > > ![screenshot.JPG](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/ac262daa9629ee434473128a17e96ca9378901cf.jpeg) ---
**Author:** ![miki](https://avatars.discourse-cdn.com/v4/letter/m/df788c/32.png) [@miki](https://gromacs.bioexcel.eu/u/miki)\ **Post date:** [September 23, 2024, 10:46am UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/6 "2024-09-23T10:46:25Z")
PS: I am re-attaching the files here in acceptable format. Thanks. > **(attachments)** > > [complex.txt](https://gromacs.bioexcel.eu/uploads/short-url/5B4SHOfaUDmMZUPOtI6sTrsK5GT.txt) (333 KB) ---
**Author:** ![miki](https://avatars.discourse-cdn.com/v4/letter/m/df788c/32.png) [@miki](https://gromacs.bioexcel.eu/u/miki)\ **Post date:** [September 23, 2024, 1:30pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/7 "2024-09-23T13:30:52Z")
I have resolved that issue. It was only a matter of ensuring the copied ligand .gro content is well aligned as you paste it in receptor.gro file. Thanks. Chukwuemeka ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 23, 2024, 1:45pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-something-is-wrong-in-the-coordinate-formatting-of-file-complex-gro/1777/8 "2024-09-23T13:45:36Z")
Great to hear!