# Urgent help: System has non-zero total charge **URL:** \ **Category:** User discussions\ **Created:** [July 12, 2023, 8:10pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823 "2023-07-12T20:10:14Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 12, 2023, 8:10pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/1 "2023-07-12T20:10:14Z")
How i can solve this issue? I read in one discussion that we can use -maxwarn option for this issue. but when i used this, it says the command line is not correct. it is showing the following warning: WARNING 1 [file topol.top, line 51]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. it showed the note: System has non-zero total charge: -0.340000 Total charge should normally be an integer. See [Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) for discussion on how close it should be to an integer. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 13, 2023, 9:07am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/2 "2023-07-13T09:07:16Z")
Could you send the exact command you used and error you got regarding the command line not being correct? Adding -maxwarn 1 to the command should work if the issue is just ignoring 1 warning. Alternatively, you could use gmx genion to add ions to neutralize the charge if it’s not necessary to the simulation ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 9:18am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/3 "2023-07-13T09:18:04Z")
I used this command: gmx grompp -f em.mdp -c solv\_ions.gro -p topol.top -o em.tpr and got the error as; NOTE 2 [file topol.top, line 51]: System has non-zero total charge: -0.340000 Total charge should normally be an integer. See [Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) for discussion on how close it should be to an integer. WARNING 1 [file topol.top, line 51]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. There were 2 notes There was 1 warning * * * Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. 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) ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 9:20am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/4 "2023-07-13T09:20:54Z")
after the command that i mentioned i just add -maxwarn and press enter then it says command not found ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 13, 2023, 9:26am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/5 "2023-07-13T09:26:10Z")
Did you include the number of warnings to ignore? (-maxwarn 1) ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 9:39am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/6 "2023-07-13T09:39:14Z")
I just used this command and i worked…i was not using 1 But as by using this warning was ignored. Is there any other way to solve the problem ? ---
**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 13, 2023, 9:45am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/7 "2023-07-13T09:45:25Z")
Do not override the warning. The fractional charge is unphysical and it means your topology is wrong. If your system is a protein, you likely chose the wrong patches for at least one terminus. Please give us the details of how you generated the topology and what terminus types you used. ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 9:53am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/8 "2023-07-13T09:53:32Z")
actually i am using a aromatase protein (PDB: 3eqm) this protein has Hem group inside it in addition to ligand. i want to do the simulation of my compound with the protein but i also wanted that hem group to be present inside the protein When i generated the topology file for the protein having Hem group then in addition to posre, topol and processed file i also got two other topolo itp files which named as topol\_Other\_chain\_A2 and topol\_Protein\_chain\_A ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 9:55am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/9 "2023-07-13T09:55:38Z")
this is my topology file : ; ; File ‘topol.top’ was generated ; By user: unknown (1000) ; On host: DESKTOP-3FJM5T1 ; At date: Thu Jul 13 00:44:12 2023 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: ; ; Executable: /usr/bin/gmx ; Data prefix: /usr ; Working dir: /mnt/c/users/Qc/Desktop/Heme-MD ; Command line: ; gmx pdb2gmx -f pro.pdb -o pro\_processed.gro -ter -ignh -missing ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include “charmm27.ff/forcefield.itp” #include “lig.itp” ; Include chain topologies #include “topol\_Protein\_chain\_A.itp” #include “topol\_Other\_chain\_A2.itp” ; Ligand position restraints #ifdef POSRES\_LIG #include “posre\_lig.itp” #endif ; Include water topology #include “charmm27.ff/tip3p.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 “charmm27.ff/ions.itp” [system] ; Name Protein in water [molecules] ; Compound #mols Protein\_chain\_A 1 Other\_chain\_A2 1 lig 1 SOL 17628 NA 1 while the information regarding the dihedrals and other stuff are present in the files that i mentioned in previous msg ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 10:13am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/10 "2023-07-13T10:13:56Z")
@jalemkul @Karis ---
**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 13, 2023, 2:34pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/11 "2023-07-13T14:34:53Z")
The end of each `[moleculetype]` in the `.itp` files will list its net charge if it was produced by `pdb2gmx`. Check the protein topology and if it has a fractional charge, it is almost certainly because you chose incorrect terminus patching. If it is coming from the ligand (`lig.itp`), then you need to correctly assign charges. ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 13, 2023, 3:00pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/12 "2023-07-13T15:00:28Z")
i checked it…as i told you three files were generated for the protein one was topolo.top and the other two were itp files. the dihedral and bond parameters for heme group and protein were separately given in these two files. i checked the file with HEME group, it has a charge in fractional value can you lease check this, i think due to this file i am getting errors. ; ; File ‘topol\_Other\_chain\_A2.itp’ was generated ; By user: unknown (1000) ; On host: DESKTOP-3FJM5T1 ; At date: Thu Jul 13 00:44:56 2023 ; ; This is a include topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: ; ; Executable: /usr/bin/gmx ; Data prefix: /usr ; Working dir: /mnt/c/users/Qc/Desktop/Heme-MD ; Command line: ; gmx pdb2gmx -f pro.pdb -o pro\_processed.gro -ter -ignh -missing ; Force field was read from the standard GROMACS share directory. ; [moleculetype] ; Name nrexcl Other\_chain\_A2 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 600 HEM rtp HEME q -5.3 1 FE 600 HEM FE 1 0.24 55.847 2 NPH 600 HEM NA 2 -0.18 14.007 3 NPH 600 HEM NB 3 -0.18 14.007 4 NPH 600 HEM NC 4 -0.18 14.007 5 NPH 600 HEM ND 5 -0.18 14.007 6 CPA 600 HEM C1A 6 0.12 12.011 7 CPB 600 HEM C2A 7 -0.06 12.011 8 CPB 600 HEM C3A 8 -0.06 12.011 9 CPA 600 HEM C4A 9 0.12 12.011 10 CPA 600 HEM C1B 10 0.12 12.011 11 CPB 600 HEM C2B 11 -0.06 12.011 12 CPB 600 HEM C3B 12 -0.06 12.011 13 CPA 600 HEM C4B 13 0.12 12.011 14 CPA 600 HEM C1C 14 0.12 12.011 15 CPB 600 HEM C2C 15 -0.06 12.011 16 CPB 600 HEM C3C 16 -0.06 12.011 17 CPA 600 HEM C4C 17 0.12 12.011 18 CPA 600 HEM C1D 18 0.12 12.011 19 CPB 600 HEM C2D 19 -0.06 12.011 20 CPB 600 HEM C3D 20 -0.06 12.011 21 CPA 600 HEM C4D 21 0.12 12.011 22 CPM 600 HEM CHA 22 -0.1 12.011 23 CPM 600 HEM CHB 23 -0.1 12.011 24 CPM 600 HEM CHC 24 -0.1 12.011 25 CPM 600 HEM CHD 25 -0.1 12.011 26 CT3 600 HEM CMA 26 -0.27 12.011 27 CT2 600 HEM CAA 27 -0.18 12.011 28 CT2 600 HEM CBA 28 -0.28 12.011 29 CC 600 HEM CGA 29 0.62 12.011 30 OC 600 HEM O1A 30 -0.76 15.999 31 OC 600 HEM O2A 31 -0.76 15.999 32 CT3 600 HEM CMB 32 -0.27 12.011 33 CE1 600 HEM CAB 33 -0.15 12.011 34 CE2 600 HEM CBB 34 -0.42 12.011 35 CT3 600 HEM CMC 35 -0.27 12.011 36 CE1 600 HEM CAC 36 -0.15 12.011 37 CE2 600 HEM CBC 37 -0.42 12.011 38 CT3 600 HEM CMD 38 -0.27 12.011 39 CT2 600 HEM CAD 39 -0.18 12.011 40 CT2 600 HEM CBD 40 -0.28 12.011 41 CC 600 HEM CGD 41 0.62 12.011 42 OC 600 HEM O1D 42 -0.76 15.999 43 OC 600 HEM O2D 43 -0.76 15.999 ; qtot -5.34 ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 14, 2023, 6:20pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/13 "2023-07-14T18:20:55Z")
When you generated the files with pdb2gmx, was there a point where you were asked to “Select start terminus type” followed by a list of options to choose? If so, which ones did you choose? As mentioned in some of the earlier replies, an incorrect choice is a likely cause of the error. Could you provide the entire output message you got when you ran pdb2gmx? ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 14, 2023, 7:07pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/14 "2023-07-14T19:07:53Z")
terminus type means the choosing of NH3+ and COO- ? ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 14, 2023, 7:14pm UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/15 "2023-07-14T19:14:18Z")
after this step i got these files [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/yPUMQhIGR1wUos6sRO7zTCzqFfV.top) (1.1 KB) the other two files were .itp files i am unable to send that files as this system does not support them. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 15, 2023, 2:25am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/16 "2023-07-15T02:25:24Z")
Yes, you might need to check if a different choice of terminus fixes the issue ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 15, 2023, 4:35am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/17 "2023-07-15T04:35:07Z")
Which terminus i can use? What tried by not using the terminus option but again it showed the same error of non zero charge value… ---
**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 15, 2023, 4:47am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/18 "2023-07-15T04:47:09Z")
Polypeptides at neutral pH have NH3+ and COO- termini, so that’s generally what you should choose. As Karis said, providing the complete terminal output from `pdb2gmx` (including your command, everything copied and pasted) would be extremely informative for us if you’re running into problems at that point. ---
**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\ **Post date:** [July 15, 2023, 5:09am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/19 "2023-07-15T05:09:21Z")
i used these. i am facing problem at the point when i run em.mdp file it says a warning with non zero charge value i am attaching the topol.top file and other two files which were generated were .itp files… i am copy pasting the file with Heme group here. ; ; File ‘topol\_Other\_chain\_A2.itp’ was generated ; By user: unknown (1000) ; On host: DESKTOP-3FJM5T1 ; At date: Fri Jul 14 10:55:39 2023 ; ; This is a include topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: ; ; Executable: /usr/bin/gmx ; Data prefix: /usr ; Working dir: /mnt/c/Users/Qc/Desktop/Heme-MD ; Command line: ; gmx pdb2gmx -f pro.pdb -o pro\_processed.gro -ignh -missing ; Force field was read from the standard GROMACS share directory. ; [moleculetype] ; Name nrexcl Other\_chain\_A2 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 600 HEM rtp HEME q -5.3 1 FE 600 HEM FE 1 0.24 55.847 2 NPH 600 HEM NA 2 -0.18 14.007 3 NPH 600 HEM NB 3 -0.18 14.007 4 NPH 600 HEM NC 4 -0.18 14.007 5 NPH 600 HEM ND 5 -0.18 14.007 6 CPA 600 HEM C1A 6 0.12 12.011 7 CPB 600 HEM C2A 7 -0.06 12.011 8 CPB 600 HEM C3A 8 -0.06 12.011 9 CPA 600 HEM C4A 9 0.12 12.011 10 CPA 600 HEM C1B 10 0.12 12.011 11 CPB 600 HEM C2B 11 -0.06 12.011 12 CPB 600 HEM C3B 12 -0.06 12.011 13 CPA 600 HEM C4B 13 0.12 12.011 14 CPA 600 HEM C1C 14 0.12 12.011 15 CPB 600 HEM C2C 15 -0.06 12.011 16 CPB 600 HEM C3C 16 -0.06 12.011 17 CPA 600 HEM C4C 17 0.12 12.011 18 CPA 600 HEM C1D 18 0.12 12.011 19 CPB 600 HEM C2D 19 -0.06 12.011 20 CPB 600 HEM C3D 20 -0.06 12.011 21 CPA 600 HEM C4D 21 0.12 12.011 22 CPM 600 HEM CHA 22 -0.1 12.011 23 CPM 600 HEM CHB 23 -0.1 12.011 24 CPM 600 HEM CHC 24 -0.1 12.011 25 CPM 600 HEM CHD 25 -0.1 12.011 26 CT3 600 HEM CMA 26 -0.27 12.011 27 CT2 600 HEM CAA 27 -0.18 12.011 28 CT2 600 HEM CBA 28 -0.28 12.011 29 CC 600 HEM CGA 29 0.62 12.011 30 OC 600 HEM O1A 30 -0.76 15.999 31 OC 600 HEM O2A 31 -0.76 15.999 32 CT3 600 HEM CMB 32 -0.27 12.011 33 CE1 600 HEM CAB 33 -0.15 12.011 34 CE2 600 HEM CBB 34 -0.42 12.011 35 CT3 600 HEM CMC 35 -0.27 12.011 36 CE1 600 HEM CAC 36 -0.15 12.011 37 CE2 600 HEM CBC 37 -0.42 12.011 38 CT3 600 HEM CMD 38 -0.27 12.011 39 CT2 600 HEM CAD 39 -0.18 12.011 40 CT2 600 HEM CBD 40 -0.28 12.011 41 CC 600 HEM CGD 41 0.62 12.011 42 OC 600 HEM O1D 42 -0.76 15.999 43 OC 600 HEM O2D 43 -0.76 15.999 ; qtot -5.34 [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 2 6 1 2 9 1 3 10 1 3 13 1 4 14 1 4 17 1 5 18 1 5 21 1 6 7 1 6 22 1 7 8 1 7 27 1 8 9 1 8 26 1 9 23 1 10 11 1 10 23 1 11 12 1 11 32 1 12 13 1 12 33 1 13 24 1 14 15 1 14 24 1 15 16 1 15 35 1 16 17 1 16 36 1 17 25 1 18 19 1 18 25 1 19 20 1 19 38 1 20 21 1 20 39 1 21 22 1 27 28 1 28 29 1 29 30 1 29 31 1 33 34 1 36 37 1 39 40 1 40 41 1 41 42 1 41 43 1 [pairs] ; ai aj funct c0 c1 c2 c3 1 7 1 1 8 1 1 11 1 1 12 1 1 15 1 1 16 1 1 19 1 1 20 1 1 22 1 1 23 1 1 24 1 1 25 1 2 10 1 2 13 1 2 14 1 2 17 1 2 18 1 2 21 1 2 26 1 2 27 1 3 6 1 3 9 1 3 14 1 3 17 1 3 18 1 3 21 1 3 32 1 3 33 1 4 6 1 4 9 1 4 10 1 4 13 1 4 18 1 4 21 1 4 35 1 4 36 1 5 6 1 5 9 1 5 10 1 5 13 1 5 14 1 5 17 1 5 38 1 5 39 1 6 20 1 6 23 1 6 26 1 6 28 1 7 21 1 7 23 1 7 29 1 8 10 1 8 22 1 8 28 1 9 11 1 9 22 1 9 27 1 10 24 1 10 33 1 11 24 1 11 34 1 12 14 1 12 23 1 13 15 1 13 23 1 13 32 1 13 34 1 14 25 1 14 36 1 15 25 1 15 37 1 16 18 1 16 24 1 17 19 1 17 24 1 17 35 1 17 37 1 18 22 1 18 39 1 19 22 1 19 40 1 20 25 1 20 41 1 21 25 1 21 38 1 21 40 1 22 27 1 22 39 1 23 26 1 23 32 1 24 33 1 24 35 1 25 36 1 25 38 1 26 27 1 27 30 1 27 31 1 32 33 1 35 36 1 38 39 1 39 42 1 39 43 1 [angles] ; ai aj ak funct c0 c1 c2 c3 2 1 3 5 2 1 4 5 180.0 0.0 0.0 0.0 2 1 5 5 3 1 4 5 3 1 5 5 180.0 0.0 0.0 0.0 4 1 5 5 1 2 6 5 1 2 9 5 6 2 9 5 1 3 10 5 1 3 13 5 10 3 13 5 1 4 14 5 1 4 17 5 14 4 17 5 1 5 18 5 1 5 21 5 18 5 21 5 2 6 7 5 2 6 22 5 7 6 22 5 6 7 8 5 6 7 27 5 8 7 27 5 7 8 9 5 7 8 26 5 9 8 26 5 2 9 8 5 2 9 23 5 8 9 23 5 3 10 11 5 3 10 23 5 11 10 23 5 10 11 12 5 10 11 32 5 12 11 32 5 11 12 13 5 11 12 33 5 13 12 33 5 3 13 12 5 3 13 24 5 12 13 24 5 4 14 15 5 4 14 24 5 15 14 24 5 14 15 16 5 14 15 35 5 16 15 35 5 15 16 17 5 15 16 36 5 17 16 36 5 4 17 16 5 4 17 25 5 16 17 25 5 5 18 19 5 5 18 25 5 19 18 25 5 18 19 20 5 18 19 38 5 20 19 38 5 19 20 21 5 19 20 39 5 21 20 39 5 5 21 20 5 5 21 22 5 20 21 22 5 6 22 21 5 9 23 10 5 13 24 14 5 17 25 18 5 7 27 28 5 27 28 29 5 28 29 30 5 28 29 31 5 30 29 31 5 12 33 34 5 16 36 37 5 20 39 40 5 39 40 41 5 40 41 42 5 40 41 43 5 42 41 43 5 [dihedrals] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 3 1 2 6 9 3 1 2 9 9 4 1 2 6 9 4 1 2 9 9 5 1 2 6 9 5 1 2 9 9 2 1 3 10 9 2 1 3 13 9 4 1 3 10 9 4 1 3 13 9 5 1 3 10 9 5 1 3 13 9 2 1 4 14 9 2 1 4 17 9 3 1 4 14 9 3 1 4 17 9 5 1 4 14 9 5 1 4 17 9 2 1 5 18 9 2 1 5 21 9 3 1 5 18 9 3 1 5 21 9 4 1 5 18 9 4 1 5 21 9 1 2 6 7 9 1 2 6 22 9 9 2 6 7 9 9 2 6 22 9 1 2 9 8 9 1 2 9 23 9 6 2 9 8 9 6 2 9 23 9 1 3 10 11 9 1 3 10 23 9 13 3 10 11 9 13 3 10 23 9 1 3 13 12 9 1 3 13 24 9 10 3 13 12 9 10 3 13 24 9 1 4 14 15 9 1 4 14 24 9 17 4 14 15 9 17 4 14 24 9 1 4 17 16 9 1 4 17 25 9 14 4 17 16 9 14 4 17 25 9 1 5 18 19 9 1 5 18 25 9 21 5 18 19 9 21 5 18 25 9 1 5 21 20 9 1 5 21 22 9 18 5 21 20 9 18 5 21 22 9 2 6 7 8 9 2 6 7 27 9 22 6 7 8 9 22 6 7 27 9 2 6 22 21 9 7 6 22 21 9 6 7 8 9 9 6 7 8 26 9 27 7 8 9 9 27 7 8 26 9 6 7 27 28 9 8 7 27 28 9 7 8 9 2 9 7 8 9 23 9 26 8 9 2 9 26 8 9 23 9 2 9 23 10 9 8 9 23 10 9 3 10 11 12 9 3 10 11 32 9 23 10 11 12 9 23 10 11 32 9 3 10 23 9 9 11 10 23 9 9 10 11 12 13 9 10 11 12 33 9 32 11 12 13 9 32 11 12 33 9 11 12 13 3 9 11 12 13 24 9 33 12 13 3 9 33 12 13 24 9 11 12 33 34 9 13 12 33 34 9 3 13 24 14 9 12 13 24 14 9 4 14 15 16 9 4 14 15 35 9 24 14 15 16 9 24 14 15 35 9 4 14 24 13 9 15 14 24 13 9 14 15 16 17 9 14 15 16 36 9 35 15 16 17 9 35 15 16 36 9 15 16 17 4 9 15 16 17 25 9 36 16 17 4 9 36 16 17 25 9 15 16 36 37 9 17 16 36 37 9 4 17 25 18 9 16 17 25 18 9 5 18 19 20 9 5 18 19 38 9 25 18 19 20 9 25 18 19 38 9 5 18 25 17 9 19 18 25 17 9 18 19 20 21 9 18 19 20 39 9 38 19 20 21 9 38 19 20 39 9 19 20 21 5 9 19 20 21 22 9 39 20 21 5 9 39 20 21 22 9 19 20 39 40 9 21 20 39 40 9 5 21 22 6 9 20 21 22 6 9 7 27 28 29 9 27 28 29 30 9 27 28 29 31 9 20 39 40 41 9 39 40 41 42 9 39 40 41 43 9 [dihedrals] ; ai aj ak al funct c0 c1 c2 c3 1 9 6 2 2 1 13 10 3 2 1 17 14 4 2 1 21 18 5 2 2 22 7 6 2 2 9 8 7 2 2 6 7 8 2 2 23 8 9 2 2 9 23 10 2 2 6 22 21 2 3 10 23 9 2 3 23 11 10 2 3 13 12 11 2 3 10 11 12 2 3 24 12 13 2 3 13 24 14 2 4 14 24 13 2 4 24 15 14 2 4 17 16 15 2 4 14 15 16 2 4 25 16 17 2 4 17 25 18 2 5 21 22 6 2 5 18 25 17 2 5 25 19 18 2 5 21 20 19 2 5 18 19 20 2 5 22 20 21 2 6 2 9 8 2 7 6 2 9 2 7 6 8 27 2 8 7 9 26 2 10 3 13 12 2 11 10 3 13 2 11 10 12 32 2 12 11 13 33 2 14 4 17 16 2 15 14 4 17 2 15 14 16 35 2 16 15 17 36 2 18 5 21 20 2 19 18 5 21 2 19 18 20 38 2 20 19 21 39 2 29 28 31 30 2 41 40 43 42 2 ; Include Position restraint file #ifdef POSRES #include “posre\_Other\_chain\_A2.itp” [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/yPUMQhIGR1wUos6sRO7zTCzqFfV.top) (1.1 KB) ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 15, 2023, 5:36am UTC](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823/20 "2023-07-15T05:36:28Z")
Terminal output as in the messages you got when you entered the commands (so the warnings, error messages, notes, etc.), just copy paste everything that shows up when you ran pdb2gmx including the exact command you used [Next page](https://gromacs.bioexcel.eu/t/urgent-help-system-has-non-zero-total-charge/6823.md?page=2)