# Fatal error with ''grompp'' **URL:** \ **Category:** User discussions\ **Created:** [June 13, 2020, 12:42pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301 "2020-06-13T12:42:52Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 13, 2020, 12:42pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/1 "2020-06-13T12:42:52Z")
GROMACS version:2020.1 GROMACS modification: No Dear friends, I want to run a simulation of DPC micelle with 65 molecules and a peptide within it. Like [DPPC and KALP tutorial](http://www.mdtutorials.com/gmx/membrane_protein/01_pdb2gmx.html) i tried to do it. I made a topology for pure DPC as I learnt from the tutorial : #include “gromos53a6-lipid.ff/forcefield.itp” #include “dpc.itp” #include “gromos53a6-lipid.ff/spc.itp” #include “gromos53a6-lipid.ff/ions.itp” [system] 65-Lipid DPC Micelle [molecules] DPC 65 SOL 6305 But after I used grompp, these warning and fatal error appeared. ![Screenshot from 2020-05-21 02-39-13](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/eacb6c5889544dd6dae0f9386540fd1bf5dbcb69.png) Thank you. VERY Newbie! ---
**Author:** ![Ali](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ali/32/170_2.png) [@Ali](https://gromacs.bioexcel.eu/u/Ali)\ **Post date:** [June 13, 2020, 1:22pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/2 "2020-06-13T13:22:32Z")
That is actually very simple. As the error is self-explaining, you have 20410 coordinates in your coordinate file (pdb), while you have specified 22880 ones in the topology. This means that either your topology includes more atoms, or your structure file includes less than expected. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 13, 2020, 1:58pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/3 "2020-06-13T13:58:34Z")
thanks for your attention. I downloaded my pdb file from [here](http://wcm.ucalgary.ca/tieleman/downloads) as it shows, it has 65 DPC molecules and 6305 water molecules. Then I wrote my topol-dpc.topology as I wrote it above in the topic, I think something else is wrong. ---
**Author:** ![Ali](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ali/32/170_2.png) [@Ali](https://gromacs.bioexcel.eu/u/Ali)\ **Post date:** [June 13, 2020, 3:05pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/4 "2020-06-13T15:05:14Z")
are you using `pdb2gmx` to generate the topology? I think you want to follow [this](http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html) tutorial to generate the right topology for your system. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 13, 2020, 4:03pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/5 "2020-06-13T16:03:19Z")
Yes. I use pdb2gmx and I follow [this](http://www.mdtutorials.com/gmx/membrane_protein/01_pdb2gmx.html) tutorial. ---
**Author:** ![Ali](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ali/32/170_2.png) [@Ali](https://gromacs.bioexcel.eu/u/Ali)\ **Post date:** [June 13, 2020, 4:33pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/6 "2020-06-13T16:33:06Z")
can you share your files? pdb and topology… through a box or drive ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 14, 2020, 10:53am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/7 "2020-06-14T10:53:58Z")
[here](https://wcm.ucalgary.ca/tieleman/files/tieleman/m65.pdb) is pdb of my main structure, and [this](https://files.rcsb.org/download/1G89.pdb) is pdb of peptide within the structure. [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/A8ZokvRKTsQ377voPTy7D0t2pa9.top) (44.1 KB) [topol-dpc.top](https://gromacs.bioexcel.eu/uploads/short-url/thWIdvlgE1Uc0ODA4h1q6JsykRy.top) (498 Bytes) [minim (copy).mdp](https://gromacs.bioexcel.eu/uploads/short-url/sFRThFXjSlRTIkydhq6DaqEG1wG.mdp) (173 Bytes) again thank you for your help. ---
**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 15, 2020, 1:43am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/8 "2020-06-15T01:43:51Z")
You haven’t included the dpc.itp file, which is important for determining any possible differences. You don’t need to do this minimization though; that’s somewhat unique to the tutorial, which starts from “broken” bilayer coordinates. Your micelle isn’t broken across periodic boundaries. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 15, 2020, 9:02am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/9 "2020-06-15T09:02:45Z")
I downloaded [dpc.itp](http://s12.picofile.com/d/8400113434/9724e9cc-cf61-401f-b6bb-f4a0f8ac2dd2/dpc.itp) file from ATB. I have forgotten to added dpc.itp to my topology. After topology correction, again I have the same problem. ---
**Author:** ![Ali](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ali/32/170_2.png) [@Ali](https://gromacs.bioexcel.eu/u/Ali)\ **Post date:** [June 15, 2020, 11:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/10 "2020-06-15T11:12:56Z")
Then here is the problem. The PDB file of your m65 does not contain all the dpc atoms in one residue. You have 65 dpc molecules which equals 3965 atoms (61 atoms each). While you only have 23 atoms in each DPC residue embedded in the m65.pdb. The difference is 2470 atoms which is what GROMACS is complaining about. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [June 20, 2020, 10:53am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/11 "2020-06-20T10:53:13Z")
Dear Ali As you told me, I used Avogadro to add Hydrogen atoms to DPC molecules but received this error. Do you know any other software or other way to solve this? [This](http://s12.picofile.com/d/8400582976/476c4861-72e7-40eb-85b8-04047050ba0a/dpcmicelle_tar.xz) is my new pdb file. ![Screenshot from 2020-06-20 15-02-28](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/3d58b46e24bded0a83d36d1d9d936787a73a7a21.png) ---
**Author:** ![Ali](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ali/32/170_2.png) [@Ali](https://gromacs.bioexcel.eu/u/Ali)\ **Post date:** [June 20, 2020, 11:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/301/12 "2020-06-20T11:12:15Z")
Well from the first look, it seems to me that you have added 53 extra atoms somewhere. Just compare the first residue in your dpcmicelle.pdb with the atoms in the dpc.itp. What you want to look is differences between the residues in the micelle and the .itp file. The new pdb file you added still has problems. have a look at this to understand more about the pdb format if you haven’t already ([https://zhanglab.ccmb.med.umich.edu/SSIPe/pdb\_atom\_format.html](https://zhanglab.ccmb.med.umich.edu/SSIPe/pdb_atom_format.html)) check the residue number 1 in the micelle for instance, there is only 23 atoms in it. while it should contain 61 atoms. I don’t know where you have added the hydrogens but both the old and new micelle files look still the same. In other words, you must have the same atoms in lines 64-124 of the dpc.itp, for all the residues in dpcmicelle.pdb. but only checking the first residue (rows 3-25) of the dpcmicelle.pdb says that your system lacks some atoms.