.gro to .pdb File Conversion Using gmx editconf and Other Tools

User discussions
1

GROMACS version: gmx 2023.3
GROMACS modification: No

Hello all,

I am doing some GROMACS runs, and in the end, I get a .gro with all the solvents, ions, and structures. Whenever I go to convert this .gro file to .pdb using:

gmx editconf -f md.gro -o output.pdb -label A

I got back something that seems to be missing structural information. I have attached an image that shows my input file in green + blue, the produced .gro file in pink, and the converted .pdb in yellow. You can see what I am referring to in the yellow structure.

image
image1397×306 105 KB

I also tried using MDAnaylsis to write the .gro to a .pdb and got the same result as the yellow structure. I am having trouble finding resources from others with similar issues. Any help would be welcome. Thank you!

2

Hello, I am going through the same problem when converting my gro file to pdb file. I tried converting the file to pdb by using pymol, gmx editconf and pdb-tools but my output is just like yours, missing structural information. I wonder if you could fix this problem. Thank you.

3

Hi,

I have never had this experience but you can use (open babel) app to convert different formats.

http://openbabel.org/index.html