# Gromacs topology error **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [May 8, 2023, 12:43pm UTC](https://gromacs.bioexcel.eu/t/gromacs-topology-error/6354 "2023-05-08T12:43:03Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Rochik](https://avatars.discourse-cdn.com/v4/letter/r/ecc23a/32.png) [@Rochik](https://gromacs.bioexcel.eu/u/Rochik)\ **Post date:** [May 8, 2023, 12:43pm UTC](https://gromacs.bioexcel.eu/t/gromacs-topology-error/6354/1 "2023-05-08T12:43:03Z")
GROMACS version: 2020.3 Hello guys, I’m working on a system of an enzyme+ two ligands. I have topology and coordinate files of the protein in Amber format and by using acpype I converted them to gromacs format. I also have the .itp files of the ligands on my directory. I want Gromacs to read a force filed (amber14SB) from my directory. This is my topology file that I made some changes, for example I included the .itp files of the ligands. ; Include forcefield parameters #include “amber14sb\_OL15.ff/forcefield.itp” ; Include ligands topology #include “lg1.itp” ; Include ligands topology #include “lg2.itp” [atomtypes] ;name bond\_type mass charge ptype sigma epsilon Amb N3 N3 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 CX CX 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 HP HP 0.00000 0.00000 A 1.95998e-01 6.56888e-02 ; 1.10 0.0157 A2C A2C 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 HC HC 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 A3C A3C 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 XC XC 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 C8 C8 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 CO CO 0.00000 0.00000 A 8.90899e-02 4.18400e-02 ; 0.50 0.0100 O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 C\* C\* 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CW CW 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 NA NA 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CN CN 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 S S 0.00000 0.00000 A 3.53241e-01 1.18156e+00 ; 1.98 0.2824 SH SH 0.00000 0.00000 A 3.53241e-01 1.18156e+00 ; 1.98 0.2824 CC CC 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CR CR 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 HS HS 0.00000 0.00000 A 1.08903e-01 5.18816e-02 ; 0.61 0.0124 CV CV 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [moleculetype] ;name nrexcl protein 3 [atoms] ; nr type resi res atom cgnr charge mass ; qtot bond\_type 1 N3 1 LEU N 1 0.101000 14.01000 ; qtot 0.101 2 H 1 LEU H1 2 0.214800 1.00800 ; qtot 0.316 3 H 1 LEU H2 3 0.214800 1.00800 ; qtot 0.531 4 H 1 LEU H3 4 0.214800 1.00800 ; qtot 0.745 5 CX 1 LEU CA 5 0.010400 12.01000 ; qtot 0.756 6 HP 1 LEU HA 6 0.105300 1.00800 ; qtot 0.861 7 A2C 1 LEU CB 7 -0.024400 12.01000 ; qtot 0.837 . . . . . . . ; Include Position restraint file #ifdef POSRES #include “posre.itp” #endif ; Include water topology #include “amber99sb.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 “amber99sb.ff/ions.itp” [system] ; Name Protein in water [molecules] ; Compound nmols Protein 1 lg1 1 lg2 1 But, at the step of adding ions to the system, I saw this error: Fatal error: Syntax error - File topol.top, line 11 Last line read: ‘[atomtypes]’ Invalid order for directive atomtypes. Could you please let me know what should I do now? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [May 8, 2023, 12:55pm UTC](https://gromacs.bioexcel.eu/t/gromacs-topology-error/6354/2 "2023-05-08T12:55:42Z")
I assume lg1.itp and lg2.itp define moleculetypes. That should happen after defining the atomtypes. So move those to includes to after the atomtypes section. ---
**Author:** ![Rochik](https://avatars.discourse-cdn.com/v4/letter/r/ecc23a/32.png) [@Rochik](https://gromacs.bioexcel.eu/u/Rochik)\ **Post date:** [May 8, 2023, 1:03pm UTC](https://gromacs.bioexcel.eu/t/gromacs-topology-error/6354/3 "2023-05-08T13:03:46Z")
Thank you so much, you’re right. It worked!