Fatal error: lnvalid line in complex.gro for atom 23403 during DEFINING UNIT CELL

User discussions
1

GROMACS version:2022.1
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 23403:

The gro file that I couldn’t protein correctly using gmx pdb2gmx -f c1.pdb -o c1.gro -ter creates the gro file correctly when I use gmx pdb2gmx -f c1.pdb -o c1.gro -ter -ignh, and also creates the complex.gro file according to the instructions.

image
image574×954 20.1 KB

3

Hi the above link can be viewed by anyone, complex.gro and protein.gro file to discover fatal error:

Invalid line in complex.gro for atom 23403 appears

Thanks:)

4

Hi Louis, the files still require permission to access

5

I changed the permissions.

6

thank you

7

Does it work if you remove the empty line you highlighted separating the 2 molecules?

8

As well as the empty line before the box dimensions.

10

thank you

11

After I followed the tutorial on solvation and added ions, I ran gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr with the fatal error: the largest distance between excuded atoms is 6.113nm. Thank you.

QQ图片20240816162249
QQ图片202408161622491099×1036 105 KB

12

Thank you.

13

If you visualize the system in VMD, does the periodic box look correct? Use the options in the Periodic tab in Graphical Representations. Are there are gaps between the periodic cells or overlaps between them?

14

After I did both of the following correctly
gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic
gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
, error running gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr.

1
11398×882 42.3 KB

2
21459×1032 60.4 KB

1
11398×882 42.3 KB

Here are the related files including topol.top, newbox.gro, ions.mdp.

Thank you

15

Thanks. I’ll check it out.

16

In vmd it shows the following,Thanks.

12
121920×1223 320 KB

17

I’d found a post where someone encountered a similar issue, apparently it’s one specific to the version of gromacs you’re using

18

thanks