# Energy minimization errors **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, mdrun\ **Created:** [June 25, 2022, 12:09am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-errors/4359 "2022-06-25T00:09:20Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![weamalyoubi](https://avatars.discourse-cdn.com/v4/letter/w/e9a140/32.png) [@weamalyoubi](https://gromacs.bioexcel.eu/u/weamalyoubi)\ **Post date:** [June 25, 2022, 12:09am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-errors/4359/1 "2022-06-25T00:09:20Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I am using gromacs to energy minimize the Protein-Ligand complex. I have performed all the steps as described in tutorial but I am getting this error while running grompp : gmx grompp -f em.mdp -c solv\_ions.gro -p topol.top -o em.tpr :-) GROMACS - gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/bioinfo/alp/alph Command line: gmx grompp -f em.mdp -c solv\_ions.gro -p topol.top -o em.tpr Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 [file em.mdp]: With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -1798595331 Generated 168379 of the 168490 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 118001 of the 168490 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’ Excluding 3 bonded neighbours molecule type ‘alp’ Excluding 2 bonded neighbours molecule type ‘SOL’ Excluding 3 bonded neighbours molecule type ‘NA’ Excluding 3 bonded neighbours molecule type ‘CL’ Excluding 3 bonded neighbours molecule type ‘CL’ NOTE 2 [file topol.top, line 102736]: System has non-zero total charge: -76.469988 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 102736]: 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. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 -------- -------- — Thank You — -------- -------- WARNING: Bad box in file solv\_ions.gro Generated a cubic box 15.524 x 13.978 x 10.104 Warning: atom name 177205 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177206 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177207 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177208 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177209 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177210 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177211 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177212 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177213 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177214 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177215 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177216 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177217 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177218 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177219 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177220 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177221 in topol.top and solv\_ions.gro does not match (NA - HW1) Warning: atom name 177222 in topol.top and solv\_ions.gro does not match (NA - HW2) Warning: atom name 177223 in topol.top and solv\_ions.gro does not match (NA - OW) Warning: atom name 177224 in topol.top and solv\_ions.gro does not match (NA - HW1) (more than 20 non-matching atom names) WARNING 2 [file topol.top, line 102736]: 368 non-matching atom names atom names from topol.top will be used atom names from solv\_ions.gro will be ignored NOTE 3 [file topol.top, line 102736]: In moleculetype ‘Protein\_chain\_A’ 955 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Analysing residue names: There are: 685 Protein residues There are: 1 Other residues There are: 55128 Water residues There are: 368 Ion residues Analysing Protein… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Number of degrees of freedom in T-Coupling group rest is 367329.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 144x120x96, spacing 0.108 0.116 0.105 Estimate for the relative computational load of the PME mesh part: 0.16 This run will generate roughly 14 Mb of data There were 3 notes There were 2 warnings * * * Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353) Fatal error: Too many warnings (2). 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) I want to ask about (177205), This number indicate the line in the file or what? and how can I fix this 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:** [June 25, 2022, 1:56am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-errors/4359/2 "2022-06-25T01:56:59Z")
Answered here: [Erorr in energy minimization - #4 by jalemkul](https://gromacs.bioexcel.eu/t/erorr-in-energy-minimization/4352/4) Please do not spam with duplicate topics. ---
**Author:** ![chiru](https://avatars.discourse-cdn.com/v4/letter/c/ce7236/32.png) [@chiru](https://gromacs.bioexcel.eu/u/chiru)\ **Post date:** [August 10, 2022, 8:47pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-errors/4359/3 "2022-08-10T20:47:06Z")
Hi, Jalemkul, I am working on HPC, I stucked at energy minimization while following Gromacs tutorial, could you help me out in this error. Both files (topology file and solv\_ions.gro) have CL ions. I am not able to fixing this, pls help me in this step. Thank you in advance. Generated 167799 of the 167910 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 117519 of the 167910 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’ Excluding 3 bonded neighbours molecule type ‘JZ4’ Excluding 2 bonded neighbours molecule type ‘SOL’ ERROR 1 [file topol\_1.top, line 24634]: No such moleculetype CL ---
**Author:** ![rpbgmx](https://avatars.discourse-cdn.com/v4/letter/r/4da419/32.png) [@rpbgmx](https://gromacs.bioexcel.eu/u/rpbgmx)\ **Post date:** [August 11, 2022, 6:26am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-errors/4359/4 "2022-08-11T06:26:39Z")
Hi Chiru, what I found yesterday was the following: when using the July 2021 force field port (the newest version instead of the March 2019 version that the tutorial calls for you have to change CL tot CLA to be able to run the script. See here for more info: [Tutorial Protein-Ligand Complex error](https://gromacs.bioexcel.eu/t/tutorial-protein-ligand-complex-error/4362)