# How do I solve this problem? - Fatal error in Gromacs **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdrun\ **Created:** [January 16, 2022, 6:42pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487 "2022-01-16T18:42:50Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 16, 2022, 6:42pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/1 "2022-01-16T18:42:50Z")
GROMACS version: 2021.5 GROMACS modification: No I’m trying a MD simulation between a protein and a ligand. I opteined .itp and .gro files of ligand from prodrg server and I added it in .gro and .top file of the protein. I used the CHARMM27 force field. First error, in the cubic box: WARNING: Bad box in file 1.gro. I went ahead. gmx grompp -f ions.mdp -c water\_box.gro -p 1.top -o ions.tpr → ERROR 1 [file DRGGMX.itp, line 23]: Atomtype CR1 not found. I tried with another .itp file, generated from LigParGen, the error was: ERROR: Fatal error: Syntax error - File Ligand.itp, line 3 Last line read: ‘[atomtypes]’ Invalid order for directive atomtypes. How can I bypass 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:** [January 16, 2022, 6:54pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/2 "2022-01-16T18:54:44Z")
PRODRG is for GROMOS (and no one should use it, the topologies are unacceptable) and LigParGen is for OPLS. You can’t mix and match force fields; it’s physical nonsensical even if you could make the syntax work. Follow this protocol if you want to use the CHARMM force field: [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/index.html) ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 16, 2022, 7:57pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/3 "2022-01-16T19:57:31Z")
Thanks Jalemkul, I’ve changed the protocol. I’ve used OPLS force field and LigParGen ligand.gro and ligand.itp but the problems still the same: WARNING: Bad box in file 1.gro (but i can walk along) and Fatal error: Syntax error - File CAR.itp, line 6 Last line read: ‘[atomtypes]’ Invalid order for directive atomtypes, which keeps it from going. ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 16, 2022, 7:59pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/4 "2022-01-16T19:59:36Z")
CAR.itp is the ligand.itp ---
**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:** [January 17, 2022, 2:00am UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/5 "2022-01-17T02:00:57Z")
All force field parameters must be declared before any `[moleculetype]` is introduced. Either move the `#include` statement for the ligand `.itp` such that it is the first `[moleculetype]` declared, or separate out the new parameters into a new file and `#include` it immediately after the parent force field. ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 17, 2022, 8:44am UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/6 "2022-01-17T08:44:27Z")
File ‘1.top’ was generated ; By user: unknown (1000) ; On host: LAPTOP-DEG ; At date: Sun Jan 16 20:48:16 2022 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2021.5 (-: ; ; Executable: /usr/local/gromacs/bin/gmx ; Data prefix: /usr/local/gromacs ; Working dir: /mnt/c/users/mrone/onedrive/desktop/ttrmd ; Command line: ; gmx pdb2gmx -f ttr.pdb -o 1.gro -p 1.top -water spce -ignh ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include “oplsaa.ff/forcefield.itp” [moleculetype] ; Name nrexcl Protein 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 20 ALA rtp ALA q +1.0 1 opls\_287 20 ALA N 1 -0.3 14.0027 …exc… … at the end: ; Include Position restraint file #ifdef POSRES #include “posre.itp” #endif ; Include Ligand topology #include “CAR.itp” ; Include water topology #include “oplsaa.ff/spce.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 “oplsaa.ff/ions.itp” [system] ; Name Protein in water [molecules] ; Compound #mols Protein 1 Ligand 1 SOL 10304 ​I don’t understand what the problem is, because if i move ;Include Ligand topology #include “CAR.itp” at the begging, the problem still persist. ---
**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:** [January 17, 2022, 10:52am UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/7 "2022-01-17T10:52:20Z")
Please upload the ligand `.itp` file so we can look at it. This should be the correct sequence of statements that fixes the issue: ```auto ; Include forcefield parameters #include “oplsaa.ff/forcefield.itp” ; Include Ligand topology #include “CAR.itp” ``` ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 17, 2022, 11:39am UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/8 "2022-01-17T11:39:32Z")
; ; GENERATED BY LigParGen Server ; Jorgensen Lab @ Yale University ; [atomtypes] opls\_814 C814 12.0110 0.000 A 3.50000E-01 2.76144E-01 opls\_824 H824 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_818 H818 1.0080 0.000 A 2.42000E-01 1.25520E-01 opls\_823 H823 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_804 N804 14.0070 0.000 A 3.25000E-01 7.11280E-01 opls\_815 N815 14.0070 0.000 A 3.30000E-01 7.11280E-01 opls\_817 H817 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_806 C806 12.0110 0.000 A 3.50000E-01 2.76144E-01 opls\_810 N810 14.0070 0.000 A 3.25000E-01 7.11280E-01 opls\_825 H825 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_821 H821 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_820 H820 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_801 C801 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_812 O812 15.9990 0.000 A 2.96000E-01 8.78640E-01 opls\_808 O808 15.9990 0.000 A 2.96000E-01 8.78640E-01 opls\_811 C811 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_828 H828 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_813 C813 12.0110 0.000 A 3.50000E-01 2.76144E-01 opls\_826 H826 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_800 C800 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_819 H819 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_805 C805 12.0110 0.000 A 3.50000E-01 2.76144E-01 opls\_827 H827 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_822 H822 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_803 C803 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_807 C807 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_802 N802 14.0070 0.000 A 3.25000E-01 7.11280E-01 opls\_816 H816 1.0080 0.000 A 2.42000E-01 1.25520E-01 opls\_829 H829 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_809 O809 15.9990 0.000 A 3.12000E-01 7.11280E-01 [moleculetype] ; Name nrexcl UNK 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 opls\_800 1 UNK C00 1 -0.1037 12.0110 2 opls\_801 1 UNK C01 1 -0.0442 12.0110 3 opls\_802 1 UNK N02 1 -0.5871 14.0070 4 opls\_803 1 UNK C03 1 0.0856 12.0110 5 opls\_804 1 UNK N04 1 -0.3406 14.0070 6 opls\_805 1 UNK C05 1 -0.0951 12.0110 7 opls\_806 1 UNK C06 1 0.1378 12.0110 8 opls\_807 1 UNK C07 1 0.4925 12.0110 9 opls\_808 1 UNK O08 1 -0.4454 15.9990 10 opls\_809 1 UNK O09 1 -0.5533 15.9990 11 opls\_810 1 UNK N0A 1 -1.1121 14.0070 12 opls\_811 1 UNK C0B 1 0.6179 12.0110 13 opls\_812 1 UNK O0C 1 -0.483 15.9990 14 opls\_813 1 UNK C0D 1 -0.2006 12.0110 15 opls\_814 1 UNK C0E 1 0.097 12.0110 16 opls\_815 1 UNK N0F 1 -0.9247 14.0070 17 opls\_816 1 UNK H0G 1 0.2034 1.0080 18 opls\_817 1 UNK H0H 1 0.4458 1.0080 19 opls\_818 1 UNK H0I 1 0.2264 1.0080 20 opls\_819 1 UNK H0J 1 0.1382 1.0080 21 opls\_820 1 UNK H0K 1 0.1382 1.0080 22 opls\_821 1 UNK H0M 1 0.1437 1.0080 23 opls\_822 1 UNK H0N 1 0.4829 1.0080 24 opls\_823 1 UNK H0O 1 0.5317 1.0080 25 opls\_824 1 UNK H0P 1 0.1377 1.0080 26 opls\_825 1 UNK H0Q 1 0.1377 1.0080 27 opls\_826 1 UNK H0R 1 0.0983 1.0080 28 opls\_827 1 UNK H0S 1 0.0983 1.0080 29 opls\_828 1 UNK H0T 1 0.3384 1.0080 30 opls\_829 1 UNK H0U 1 0.3384 1.0080 [bonds] 2 1 1 0.1370 435136.000 3 2 1 0.1381 357313.600 4 3 1 0.1343 399153.600 5 1 1 0.1394 343088.000 6 2 1 0.1504 265265.600 7 6 1 0.1529 224262.400 8 7 1 0.1522 265265.600 9 8 1 0.1229 476976.000 10 8 1 0.1364 376560.000 11 7 1 0.1449 282001.600 12 11 1 0.1335 410032.000 13 12 1 0.1229 476976.000 14 12 1 0.1522 265265.600 15 14 1 0.1529 224262.400 16 15 1 0.1448 319657.600 17 1 1 0.1080 307105.600 18 3 1 0.1010 363171.200 19 4 1 0.1080 307105.600 20 6 1 0.1090 284512.000 21 6 1 0.1090 284512.000 22 7 1 0.1090 284512.000 23 10 1 0.0945 462750.400 24 11 1 0.1010 363171.200 25 14 1 0.1090 284512.000 26 14 1 0.1090 284512.000 27 15 1 0.1090 284512.000 28 15 1 0.1090 284512.000 29 16 1 0.1010 363171.200 30 16 1 0.1010 363171.200 5 4 1 0.1335 408358.400 [angles] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 106.300 585.760 2 3 4 1 109.800 585.760 2 1 5 1 111.000 585.760 1 2 6 1 130.700 585.760 2 6 7 1 114.000 527.184 6 7 8 1 111.100 527.184 7 8 9 1 120.400 669.440 7 8 10 1 108.000 585.760 6 7 11 1 109.700 669.440 7 11 12 1 121.900 418.400 11 12 13 1 122.900 669.440 11 12 14 1 116.600 585.760 12 14 15 1 111.100 527.184 14 15 16 1 109.470 470.282 2 1 17 1 128.200 292.880 2 3 18 1 120.000 292.880 3 4 19 1 120.000 292.880 2 6 20 1 109.500 292.880 2 6 21 1 109.500 292.880 6 7 22 1 110.700 313.800 8 10 23 1 113.000 292.880 7 11 24 1 118.400 317.984 12 14 25 1 109.500 292.880 12 14 26 1 109.500 292.880 14 15 27 1 110.700 313.800 14 15 28 1 110.700 313.800 15 16 29 1 109.500 292.880 15 16 30 1 109.500 292.880 8 7 11 1 110.100 527.184 15 14 26 1 110.700 313.800 27 15 28 1 107.800 276.144 12 11 24 1 119.800 292.880 11 7 22 1 109.500 292.880 29 16 30 1 106.400 364.845 13 12 14 1 120.400 669.440 20 6 21 1 107.800 276.144 16 15 28 1 109.500 292.880 5 1 17 1 120.000 292.880 1 5 4 1 110.000 585.760 9 8 10 1 121.000 669.440 16 15 27 1 109.500 292.880 4 3 18 1 120.000 292.880 5 4 19 1 120.000 292.880 3 2 6 1 121.600 585.760 8 7 22 1 109.500 292.880 25 14 26 1 107.800 276.144 15 14 25 1 110.700 313.800 3 4 5 1 120.000 585.760 7 6 21 1 110.700 313.800 7 6 20 1 110.700 313.800 [dihedrals] ; IMPROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 14 12 11 13 4 180.000 43.932 2 6 2 1 3 4 180.000 10.460 2 24 11 7 12 4 180.000 10.460 2 18 3 2 4 4 180.000 10.460 2 19 4 3 5 4 180.000 10.460 2 17 1 2 5 4 180.000 10.460 2 10 8 7 9 4 180.000 43.932 2 [dihedrals] ; PROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 8 7 6 2 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 12 11 7 8 3 -2.910 -0.387 -3.816 7.113 -0.000 0.000 12 11 7 6 3 1.933 0.000 -1.933 -0.000 -0.000 0.000 4 3 2 1 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 4 5 1 2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 14 12 11 7 3 30.288 -4.812 -25.476 -0.000 -0.000 0.000 15 14 12 11 3 0.734 -9.985 -0.791 10.042 -0.000 0.000 15 14 12 13 3 0.000 0.000 0.000 -0.000 -0.000 0.000 7 6 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 7 6 2 3 3 1.046 -3.556 2.510 -0.000 -0.000 0.000 6 2 1 5 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 6 2 3 4 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 24 11 12 14 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 24 11 12 13 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 24 11 7 8 3 0.000 0.000 0.000 -0.000 -0.000 0.000 24 11 7 6 3 0.000 0.000 0.000 -0.000 -0.000 0.000 24 11 7 22 3 0.000 0.000 0.000 -0.000 -0.000 0.000 18 3 4 5 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 18 3 2 6 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 18 3 2 1 3 20.920 0.000 -20.920 -0.000 -0.000 0.000 30 16 15 14 3 -1.268 3.021 1.745 -3.498 -0.000 0.000 29 16 15 14 3 -1.268 3.021 1.745 -3.498 -0.000 0.000 30 16 15 28 3 0.837 2.510 0.000 -3.347 -0.000 0.000 30 16 15 27 3 0.837 2.510 0.000 -3.347 -0.000 0.000 29 16 15 28 3 0.837 2.510 0.000 -3.347 -0.000 0.000 29 16 15 27 3 0.837 2.510 0.000 -3.347 -0.000 0.000 19 4 3 2 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 19 4 3 18 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 19 4 5 1 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 17 1 2 6 3 44.978 0.000 -44.978 -0.000 -0.000 0.000 17 1 2 3 3 44.978 0.000 -44.978 -0.000 -0.000 0.000 17 1 5 4 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 26 14 12 11 3 0.000 0.000 0.000 -0.000 -0.000 0.000 25 14 12 11 3 0.000 0.000 0.000 -0.000 -0.000 0.000 26 14 12 13 3 0.000 0.000 0.000 -0.000 -0.000 0.000 22 7 8 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000 25 14 12 13 3 0.000 0.000 0.000 -0.000 -0.000 0.000 22 7 8 10 3 0.000 0.000 0.000 -0.000 -0.000 0.000 27 15 14 12 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 20 6 7 8 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 21 6 7 8 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 28 15 14 12 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 22 7 6 2 3 0.967 2.900 0.000 -3.866 -0.000 0.000 28 15 14 26 3 0.628 1.883 0.000 -2.510 -0.000 0.000 27 15 14 25 3 0.628 1.883 0.000 -2.510 -0.000 0.000 22 7 6 21 3 0.628 1.883 0.000 -2.510 -0.000 0.000 27 15 14 26 3 0.628 1.883 0.000 -2.510 -0.000 0.000 22 7 6 20 3 0.628 1.883 0.000 -2.510 -0.000 0.000 28 15 14 25 3 0.628 1.883 0.000 -2.510 -0.000 0.000 20 6 7 11 3 0.971 2.912 0.000 -3.883 -0.000 0.000 21 6 7 11 3 0.971 2.912 0.000 -3.883 -0.000 0.000 25 14 15 16 3 -4.096 5.088 2.966 -3.958 -0.000 0.000 26 14 15 16 3 -4.096 5.088 2.966 -3.958 -0.000 0.000 20 6 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 21 6 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 20 6 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 21 6 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 22 7 11 12 3 0.000 0.000 0.000 -0.000 -0.000 0.000 23 10 8 7 3 26.150 -3.138 -23.012 -0.000 -0.000 0.000 23 10 8 9 3 23.012 0.000 -23.012 -0.000 -0.000 0.000 11 7 8 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000 11 7 8 10 3 0.000 0.000 0.000 -0.000 -0.000 0.000 11 7 6 2 3 -0.766 2.707 4.025 -5.966 -0.000 0.000 3 4 5 1 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 5 4 3 2 3 41.840 0.000 -41.840 -0.000 -0.000 0.000 5 1 2 3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 16 15 14 12 3 3.335 -1.552 2.820 -4.602 -0.000 0.000 9 8 7 6 3 0.000 0.000 0.000 -0.000 -0.000 0.000 13 12 11 7 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 10 8 7 6 3 5.318 0.732 -2.284 -3.766 -0.000 0.000 [pairs] 1 7 1 4 6 1 3 7 1 2 8 1 5 6 1 2 11 1 6 9 1 6 10 1 6 12 1 1 18 1 9 11 1 8 12 1 7 13 1 3 17 1 1 19 1 10 11 1 7 14 1 4 17 1 2 19 1 1 20 1 1 21 1 6 17 1 5 18 1 3 20 1 6 18 1 3 21 1 2 22 1 11 15 1 13 15 1 12 16 1 8 20 1 8 21 1 7 23 1 6 24 1 11 20 1 9 22 1 11 21 1 10 22 1 9 23 1 8 24 1 12 22 1 11 25 1 18 19 1 13 24 1 11 26 1 14 24 1 13 25 1 13 26 1 12 27 1 12 28 1 16 25 1 20 22 1 16 26 1 21 22 1 14 29 1 14 30 1 22 24 1 25 27 1 26 27 1 25 28 1 26 28 1 27 29 1 28 29 1 27 30 1 28 30 1 ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 17, 2022, 12:10pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/10 "2022-01-17T12:10:17Z")
​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ With your new syntax, the gromacs error is: ​ ERROR 1 [file 1.top, line 18835]: No such moleculetype CAR It’s referred to the end part of .top file: [molecules] ; Compound #mols Protein 1 CAR 1 SOL 9792 ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 17, 2022, 12:11pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/11 "2022-01-17T12:11:08Z")
With your new syntax, the gromacs error is: ​ ERROR 1 [file 1.top, line 18835]: No such moleculetype CAR It’s referred to the end part of .top file: [molecules] ; Compound #mols Protein 1 CAR 1 SOL 9792 ---
**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:** [January 17, 2022, 1:05pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/12 "2022-01-17T13:05:19Z")
The ligand `[moleculetype]` is not named CAR, it is named UNK: > [@Marco91](#): > > [moleculetype] > ; Name nrexcl > UNK 3 ---
**Author:** ![Marco91](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/marco91/32/1243_2.png) [@Marco91](https://gromacs.bioexcel.eu/u/Marco91)\ **Post date:** [January 17, 2022, 3:45pm UTC](https://gromacs.bioexcel.eu/t/how-do-i-solve-this-problem-fatal-error-in-gromacs/3487/13 "2022-01-17T15:45:26Z")
Thank u very much sir, I just created the .tpr file, i don’t know why i’ve changed the name, in my first version was UNK. I’ll try to go away!