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.
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!