# ERROR 1 \[file strong\_posre\_Protein\_chain\_A.itp, line 4414\]: INQUIRY **URL:** \ **Category:** User discussions\ **Created:** [July 7, 2022, 1:09pm UTC](https://gromacs.bioexcel.eu/t/error-1-file-strong-posre-protein-chain-a-itp-line-4414-inquiry/4435 "2022-07-07T13:09:08Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Post date:** [July 7, 2022, 1:09pm UTC](https://gromacs.bioexcel.eu/t/error-1-file-strong-posre-protein-chain-a-itp-line-4414-inquiry/4435/1 "2022-07-07T13:09:08Z")
GROMACS version: 2022.1 GROMACS modification: No Here post your question: Hello and thank you for considering this:): For the below subsection: ### Membrane Protein: KALP15 in DPPC **Step Three: Defining the Unit Cell & Adding Solvent** **2. Pack the lipids around the protein** I input the below command for an oligomeric heptamer transmembrane protein: gmx grompp -f minim\_inflategro.mdp -c system\_inflated.gro -p topol.top -r system\_inflated.gro -o system\_inflated\_em.tpr and received the following: Atom index (4410) in position\_restraints out of bounds (1-4409). 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. I HAD ADJUSTED MY TOPOL.TOP TO THE BELOW: ; ; File ‘topol.top’ was generated ; By user: joelsubach (501) ; On host: Joels-MacBook-Air.local ; At date: Fri Jun 24 19:42:53 2022 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2022.1 (-: ; ; Executable: /usr/local/bin/gmx ; Data prefix: /usr/local ; Working dir: /Users/joelsubach/Desktop/Panx1\_Membrane\_Protein ; Command line: ; gmx pdb2gmx -f GalaxyPanx1\_Seq.pdb -o GalaxyPanx1\_Seq\_processed.gro -ignh -ter -water spc ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include “gromos53a6\_lipid.ff/forcefield.itp” ; Include chain topologies #include “topol\_Protein\_chain\_A.itp” #ifdef POSRES #include “posre\_Protein\_chain\_A.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_A.itp” #endif #include “topol\_Protein\_chain\_B.itp” #ifdef POSRES #include “posre\_Protein\_chain\_B.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_B.itp” #endif #include “topol\_Protein\_chain\_C.itp” #ifdef POSRES #include “posre\_Protein\_chain\_C.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_C.itp” #endif #include “topol\_Protein\_chain\_D.itp” #ifdef POSRES #include “posre\_Protein\_chain\_D.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_D.itp” #endif #include “topol\_Protein\_chain\_E.itp” #ifdef POSRES #include “posre\_Protein\_chain\_E.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_E.itp” #endif #include “topol\_Protein\_chain\_F.itp” #ifdef POSRES #include “posre\_Protein\_chain\_F.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_F.itp” #endif #include “topol\_Protein\_chain\_G.itp” #ifdef POSRES #include “posre\_Protein\_chain\_G.itp” #endif #ifdef STRONG\_POSRES #include “strong\_posre\_Protein\_chain\_G.itp” #endif ; Include DPPC chain topology #include “dppc.itp” ; Include water topology #include “gromos53a6\_lipid.ff/spc.itp” #ifdef POSRES\_WATER ; Position restraint for each water oxygen [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include “gromos53a6\_lipid.ff/ions.itp” [system] ; Name Protein [molecules] ; Compound #mols Protein\_chain\_A 1 Protein\_chain\_B 1 Protein\_chain\_C 1 Protein\_chain\_D 1 Protein\_chain\_E 1 Protein\_chain\_F 1 Protein\_chain\_G 1 DPPC 108 and again input the below command: **Command line:** \*\* gmx grompp -f minim\_inflategro.mdp -c system\_inflated.gro -p topol.top -r system\_inflated.gro -o system\_inflated\_em.tpr\*\* **and am now getting the below error:** ERROR 1 [file strong\_posre\_Protein\_chain\_A.itp, line 4414]: Atom index (4410) in position\_restraints out of bounds (1-4409). 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. **with my strong\_posre\_Protein\_chain\_A.itp exhibiting the following:** 4401 1 100000 100000 100000 4402 1 100000 100000 100000 4403 1 100000 100000 100000 4404 1 100000 100000 100000 4405 1 100000 100000 100000 4406 1 100000 100000 100000 4407 1 100000 100000 100000 4408 1 100000 100000 100000 4409 1 100000 100000 100000 4410 1 100000 100000 100000 4411 1 100000 100000 100000 4412 1 100000 100000 100000 4413 1 100000 100000 100000 4414 1 100000 100000 100000 4415 1 100000 100000 100000 4416 1 100000 100000 100000 4417 1 100000 100000 100000 4418 1 100000 100000 100000 4419 1 100000 100000 100000 4420 1 100000 100000 100000 I believe that the error is within the TOPOL.TOP multiple restraint file formatting portion, any help from any members of this forum would be very helpful, thanks:) Joel ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 8, 2022, 1:46am UTC](https://gromacs.bioexcel.eu/t/error-1-file-strong-posre-protein-chain-a-itp-line-4414-inquiry/4435/2 "2022-07-08T01:46:27Z")
See the last paragraph of [Common errors when using GROMACS — GROMACS 2022.2 documentation](https://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds) and search the forums for this exact error. It gets asked and answered almost on a weekly basis. ---
**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Post date:** [July 9, 2022, 8:27pm UTC](https://gromacs.bioexcel.eu/t/error-1-file-strong-posre-protein-chain-a-itp-line-4414-inquiry/4435/3 "2022-07-09T20:27:49Z")
Hi Justin thank you so much for your kind update and problem solved (I used your thread with Sumedha).