GROMACS version:2020.3
GROMACS modification: Yes/No
Here post your question:
Protein-Ligand Complex-Define Box and Solvate:
during the command:
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
the below fatal error occurs:
Invalid line in complex.gro for atom 2615 appears, however, I followed the instructions correctly for creating the complex.gro file (see below):
163ASN C 2612 0.621 -0.740 -0.126
163ASN OT1 2613 0.624 -0.616 -0.140
163ASN OT2 2614 0.683 -0.703 -0.011
1JZ4 C1 1 2.429 -2.412 -0.007
1JZ4 C2 2 2.155 -2.721 -0.411
1JZ4 C3 3 2.207 -2.675 -0.533
1JZ4 C4 4 2.267 -2.551 -0.545
1JZ4 C9 5 2.277 -2.473 -0.430
1JZ4 O10 6 2.169 -2.646 -0.295
1JZ4 H22 7 2.229 -2.519 -0.308
1JZ4 C8 8 2.246 -2.441 -0.181
1JZ4 H21 9 2.392 -2.470 -0.139
1JZ4 C5 10 2.341 -2.354 -0.434
1JZ4 H18 11 2.531 -2.436 0.015
1JZ4 C6 12 2.366 -2.453 0.069
1JZ4 H19 13 2.417 -2.306 -0.010
1JZ4 C7 14 2.107 -2.812 -0.407
1JZ4 H20 15 2.199 -2.735 -0.617
1JZ4 H1 16 2.304 -2.518 -0.635
1JZ4 H2 17 2.137 -2.681 -0.204
1JZ4 H3 18 2.178 -2.476 -0.106
1JZ4 H4 19 2.227 -2.337 -0.193
1JZ4 H5 20 2.458 -2.429 -0.214
1JZ4 H6 21 2.402 -2.577 -0.131
1JZ4 H7 22 2.374 -2.321 -0.516
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000
I also renamed each atom i.e. 1-2615, 2-2616 and the same error was exhibited?
Suggestions?
Thanks:)
Hi,
It looks like your file has a bad formatting. Please have a look at the gro file format here http://manual.gromacs.org/current/reference-manual/file-formats.html#gro
Best regards
Alessandra
Hi Alessandra and thank you for your kind update and that pasted inaccurately, please see screenshot attached
I think it is a different problem
What is the number of atoms listed on line 2 of the .gro file? If it hasn’t been updated correctly, it will cause any GROMACS program to try to read box information from the line that contains coordinates of atom 2615.
Hi Justin and thank you for your kind update and yes I originally updated the number of atoms accordingly to 2636 which should be correct.
Please upload the file somewhere so we can look at it.
Hello and thank you, I am still very new at this accordingly are there any choices that you may recommend on where I can load this file where it would be easiest for you to view?
Thanks:)
Attach to a post here, upload to Google Drive, or whatever file-sharing server you prefer.
Hello thanks and ok what would be the specific name of the ´people and groups´ to be Google Drive shared with please?
You don’t need to set any specific restrictions like that. Just make the link accessible to anyone. It’s a tutorial system, nothing proprietary that requires security.
Hi the above link can be viewed by anyone, complex.gro file to discover fatal error:
Invalid line in complex.gro for atom 2615 appears
Much Thanks:)
Somehow you’ve duplicated the protein coordinates in complex.gro:
163ASN C 2612 0.621 -0.740 -0.126
163ASN OT1 2613 0.624 -0.616 -0.140
163ASN OT2 2614 0.683 -0.703 -0.011
LYSOZYME
2614
1MET N 1 0.556 -1.596 -0.893
1MET H1 2 0.522 -1.511 -0.855
1MET H2 3 0.520 -1.608 -0.986
I suggest you start over in copying the coordinates properly. This file is completely non-functional.
Hello and thank you for your kind update and I will examine my errors more carefully in the future to manage your time, apologies, thanks:)
Fatal error:
Unexpected end of file in file AKT1solv.gro at line 69973
I have the same problem as you, how did you solve it?
Hi Wang thank you for your message, that was quite some time ago but I believe I was pasting and or copying twice by mistake
or something like that.
Kind Regards,
Joel 🚀
Hi, thanks for your prompt reply. I have solved this problem. My mistake was wrong use of spc/e when outputting gro files.
same situation met by me, check the molecule number in your .gro file and top file. Especially when you use gmx solvate, the number of water molecules in .top file should be decreased.
gmx read the last line as atom while actually it’s the end line of coordinates.
