# Restrains positions issue of metal ions in protein active site **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, simulation-setup\ **Created:** [November 4, 2023, 3:36pm UTC](https://gromacs.bioexcel.eu/t/restrains-positions-issue-of-metal-ions-in-protein-active-site/7548 "2023-11-04T15:36:36Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Zahraibt7](https://avatars.discourse-cdn.com/v4/letter/z/7ea924/32.png) [@Zahraibt7](https://gromacs.bioexcel.eu/u/Zahraibt7)\ **Post date:** [November 4, 2023, 3:36pm UTC](https://gromacs.bioexcel.eu/t/restrains-positions-issue-of-metal-ions-in-protein-active-site/7548/1 "2023-11-04T15:36:36Z")
GROMACS version:2021 GROMACS modification: Yes/No Here post your question Hi all, I have prepared my metalloprotein-inhibitor model with CHARMM-GUI and need to restrains positions of Zn atoms. I have tried two different methods and got the same error for both of them: 1. Adding these lines into ZN2.itp file in toppar folder: #ifdef POSRES\_ZN [position\_restraints] ; i funct fcx fcy fcz 10952 1 1000 1000 1000 10953 1 1000 1000 1000 #endif 2. Adding these lines into topol.top file: ; Include forcefield parameters #include “toppar/forcefield.itp” #include “toppar/PROA.itp” #include “toppar/ZN2.itp” #ifdef POSRES\_ZN #include “posre\_zn.itp” #endif #include “toppar/LHK.itp” #include “toppar/SOD.itp” #include “toppar/CLA.itp” #include “toppar/TIP3.itp” ERROR 1 [file ZN2.itp, line 22]: Atom index (10952) in position\_restraints out of bounds (1-1). This probably means that you have inserted topology section “position\_restraints” in a part belonging to a different molecule than you intended to. In that case move the “position\_restraints” section to the right molecule. Any help/suggest will be appreciated Bests Zahra ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [November 5, 2023, 7:26pm UTC](https://gromacs.bioexcel.eu/t/restrains-positions-issue-of-metal-ions-in-protein-active-site/7548/2 "2023-11-05T19:26:56Z")
Hi Zahra, Based on the error, it seems that your `ZN2.itp` has just one atom (or perhaps two atoms) defined in the `[atoms]` section following the `[moleculetype]` with zinc ions. In that case, you should use numbering from that `[atoms]` section, so if there are two atoms, use `1` and `2` instead of `10952` and `10953`. Note that `[atoms]` for each molecule defined in the topology have to have numbering starting with 1, so even if your `ZN2.itp` has different numbers, make sure to renumber it. (This is all assuming that adding position restraints to zinc atoms only is what you want to do - keep in mind it will restrain them to their spatial location, but other parts of the system will be able to move freely.) Best, MW ---
**Author:** ![Zahraibt7](https://avatars.discourse-cdn.com/v4/letter/z/7ea924/32.png) [@Zahraibt7](https://gromacs.bioexcel.eu/u/Zahraibt7)\ **Post date:** [November 6, 2023, 6:00am UTC](https://gromacs.bioexcel.eu/t/restrains-positions-issue-of-metal-ions-in-protein-active-site/7548/3 "2023-11-06T06:00:20Z")
Dear Milosz, Hi. Thank you so much for your reply. I have used the following command line to make posre\_ZN.itp file so 10952 and 10953 are related to Zn atom numbers in .gro file: gmx genrestr -f step3\_input.gro -o posre\_ZN.itp -fc 1000 1000 1000 in ZN2.itp there is only one atom: [moleculetype] ; name nrexcl ZN2 1 [atoms] ; nr type resnr residu atom cgnr charge mass 1 ZN 751 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0 So I have changed it to: [atoms] ; nr type resnr residu atom cgnr charge mass 1 ZN 751 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0 2 ZN 752 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0 #ifdef POSRES\_ZN [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 2 1 1000 1000 1000 #endif Using above mentioned ZN2.itp, I got this issue at the minimization step: Fatal error: number of coordinates in coordinate file (step3\_input.gro, 132816) does not match topology (topol.top, 132818) For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) Can you please let know how to fix this issue. I appreciate your time and consideration Bests Zahra ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [November 6, 2023, 3:53pm UTC](https://gromacs.bioexcel.eu/t/restrains-positions-issue-of-metal-ions-in-protein-active-site/7548/4 "2023-11-06T15:53:11Z")
Hi Zahra, if your ZN2.itp only had 1 atom, then it could be fine too - the name was ambiguous as there’s a ZN2 residue but that could also be 2x ZN. Now that you made a `ZN2` molecule that has two atoms in it, your `[system]` directive probably contains this molecule twice, so `grompp` will think there are 2x2 = 4 Zn ions while your `.gro` has only 2. Either decrease the number of `ZN2` molecules in `[system]` or make your `ZN2` with one atom only.