# Gmx editconf and number of atom limit **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools, simulation-setup\ **Created:** [July 17, 2023, 10:19am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846 "2023-07-17T10:19:49Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![fredpontes20](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@fredpontes20](https://gromacs.bioexcel.eu/u/fredpontes20)\ **Post date:** [July 17, 2023, 10:19am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/1 "2023-07-17T10:19:49Z")
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 ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 18, 2023, 7:03am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/2 "2023-07-18T07:03:07Z")
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?](https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-November/117062.html) and [[gmx-users] maximum number of molecules](https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/HQyqXatq/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 ---
**Author:** ![fredpontes20](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@fredpontes20](https://gromacs.bioexcel.eu/u/fredpontes20)\ **Post date:** [July 18, 2023, 7:44am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/3 "2023-07-18T07:44:47Z")
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?" ---
**Author:** ![fredpontes20](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@fredpontes20](https://gromacs.bioexcel.eu/u/fredpontes20)\ **Post date:** [July 18, 2023, 7:46am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/4 "2023-07-18T07:46:00Z")
I tried to convert from pdb to gro format using gmx editconf and I found the same problem: only read 99995 atoms . ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 18, 2023, 7:54am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/5 "2023-07-18T07:54:13Z")
Does using openbabel to convert the file produce the same error? ([OPENBABEL - Chemical file format converter](http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html)) Also, does specifying the boxtype to fix that warning solve the issue? ---
**Author:** ![fredpontes20](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@fredpontes20](https://gromacs.bioexcel.eu/u/fredpontes20)\ **Post date:** [July 18, 2023, 8:03am UTC](https://gromacs.bioexcel.eu/t/gmx-editconf-and-number-of-atom-limit/6846/6 "2023-07-18T08:03:47Z")
I didn’t try with OpenBabel. It’s a good suggestion. I tried to convert using VMD and I got a very weird structure.