Gmx editconf and number of atom limit

User discussions
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1

GROMACS version: 5.0.7 and 2019.6
GROMACS modification: Yes/No

Hi, everyone!
I’m trying to rotate a protein with more than 120000 atoms using gmx editconf. I tried to do this using different software versions and only the first 99995 atoms were read, rotate and written on output file.
Then, I have one question: Is it a gmx editconf limitation? Is there a way to overcome this?
Thanks in advance,
Fred

2

Are you using .pdb files or .gro files? From what I could find online, it seems this may be an issue specific to .pdb files (see [gmx-users] THE max number of atoms in gromacs? and [gmx-users] maximum number of molecules), so changing to using .gro files might fix this issue.

If not, could you post the exact command you used and copy-paste the terminal outputs you got from the command? That would help with diagnosing what the issue might be

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Hi Karis,
I’m working with a pdb file and type a command like:

gmx editconf -f protein-in.pdb -box 30 30 30 -d 3.0 -rotate
0 180 0 -o protein-out.pdb

terminal outputs:

"Note that major changes are planned in future for editconf, to improve usability and utility.Read 99995 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found
system size : 24.953 25.112 16.890 (nm)
center : 14.783 14.764 13.751 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
Rotating 0, 180, 0 degrees around the X, Y and Z axis respectively
new system size : 24.953 25.112 16.890
shift : 30.260 0.792 25.196 (nm)
new center : 15.476 15.556 11.445 (nm)
new box vectors : 30.953 31.112 22.890 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume :22043.29 (nm^3)

WARNING: No boxtype specified - distance condition applied in each dimension.
If the molecule rotates the actual distance will be smaller. You might want
to use a cubic box instead, or why not try a dodecahedron today?"

4

I tried to convert from pdb to gro format using gmx editconf and I found the same problem: only read 99995 atoms .

5

Does using openbabel to convert the file produce the same error? (OPENBABEL - Chemical file format converter)

Also, does specifying the boxtype to fix that warning solve the issue?

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I didn’t try with OpenBabel. It’s a good suggestion. I tried to convert using VMD and I got a very weird structure.