Invalid order for directive atomtypes (error)

User discussions
1

GROMACS version: 2019.4
GROMACS modification: No
Here post your question

Hi GMX users,

In my studied system there are 2 types of small molecules (LIG and POV). I prepared the itp files for them using antechamber module. Topol.top and pov.itp and lig.itp files are as follows:

; Include forcefield parameters
#include “amber03.ff/forcefield.itp”

[ moleculetype ]
; Name nrexcl
complex 3

; Include pov topology
#include “pov.itp”

; Include lig topology
#include “lig.itp”

; Include water topology
#include “amber03.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 “amber03.ff/ions.itp”

[ system ]
; Name
pov-lig in water

[ molecules ]
; Compound #mols
LIG 2
POV 2

pov.itp

lig.itp

After following coommand I encountered with error:
gmx_mpi grompp -f em1.mdp -c sol.gro -p topol.top -o em1.tpr

Program: gmx grompp, version 2019.4
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 607)

Fatal error:
Syntax error - File pov.itp, line 1
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes

How to fix this issue?

Best,
Merry

2

If your ligand topologies both introduce new atom types (or any other force field parameters), you have to collect them and declare those directives before any [moleculetype] can be introduced. The entire force field has to be complete before any molecules can be defined. See the Error FAQ page for more information.

3

Dear Justin,
Thanks for your answer. You are right. In first lines of both itp file of my ligands there are [atomtypes]. I collected them and put them in the first lines of topol.top file, as follows:

[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
n4 n4 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
p5 p5 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000
c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
os os 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700
o o 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
c2 c2 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157
h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157
hx hx 0.00000 0.00000 A 1.95998e-01 6.56888e-02 ; 1.10 0.0157
ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
h2 h2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157
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
ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
cf cf 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860

; Include pov topology
#include “pov.itp”

; Include lig topology
#include “lig.itp”

; Include water topology
#include “amber03.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 “amber03.ff/ions.itp”

[ system ]
; Name
pov-lig in water

[ molecules ]
; Compound #mols
POV 2
LIG 2

Now, there is no [atomtypes] in pov.itp and lig.itp and these files starts with:

[ moleculetype ]
;name nrexcl
POV 3

[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 n4 1 POV N 1 -0.582801 14.01000 ; qtot -0.583
2 p5 1 POV P 2 1.447798 30.97000 ; qtot 0.865
3 c3 1 POV C1 3 0.159400 12.01000 ; qtot 1.024
.
.
.

Thus, [atomtypes] is before any [moleculetype]. But I have the same error as before:

Fatal error:
Syntax error - File topol.top, line 1
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes

How to fix it?

Best,
Merry

4

The first valid directive in any topology is [defaults], which governs all aspects of the energy function and how topology entries are interpreted. You can either enter this by hand, or, since it appears you are using AMBER ion parameters, just #include the parent AMBER force field itself, then declare new [atomtypes] and the rest of the topology.

5

Dear Justin,
Many thanks for your useful guidance. My problem was solved by including the parent AMBER force field in the topol.top file.

Best,
Merry

6

Dear Jalemkul,
I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each molecule are given below. Kindly help me out. I am new to Gromacs.

Fatal error:
Syntax error - File receptor.itp, line 8
Last line read:
‘[ atomtypes ] ’
Invalid order for directive atomtypes’

My topol.top file looks like below:

; Include forcefield parameters
#include “charmm27.ff/forcefield.itp”

; Include drg topology
#include “H2PO4.itp”

; Include lig topolgy
#include “receptor.itp”

; 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
System in water

[ molecules ]
; Compound #mols
LIG 1
DRG 1
SOL 6436

The two .itp files mentioned for those two molecules are as follows:

H2PO4.itp

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
PO4 15 30.9738 0.0 A 0.383086 2.447640
O2CM 8 15.9994 0.0 A 0.302905 0.502080
OR 8 15.9994 0.0 A 0.315378 0.636386
HOCO 1 1.0079 0.0 A 0.040001 0.192464

[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS

[ moleculetype ]
; Name nrexcl
DRG 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 PO4 1 DRG P 1 1.7089 30.9738
2 O2CM 1 DRG O 2 -0.9718 15.9994
3 O2CM 1 DRG O1 3 -0.8613 15.9994
4 OR 1 DRG O2 4 -0.8821 15.9994
5 OR 1 DRG O3 5 -0.8625 15.9994
6 HOCO 1 DRG H 6 0.4341 1.0079
7 HOCO 1 DRG H1 7 0.4347 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
5 6 1 0.09810 445818.6 0.09810 445818.6
5 1 1 0.16300 315740.5 0.16300 315740.5
2 1 1 0.15100 499596.4 0.15100 499596.4
1 3 1 0.15100 499596.4 0.15100 499596.4
1 4 1 0.16300 315740.5 0.16300 315740.5
4 7 1 0.09810 445818.6 0.09810 445818.6

[ pairs ]
; ai aj fu
2 7 1
2 6 1
3 7 1
3 6 1
4 6 1
5 7 1

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 122.8570 751.56 122.8570 751.56
2 1 4 1 109.6880 903.91 109.6880 903.91
2 1 5 1 109.6880 903.91 109.6880 903.91
3 1 4 1 109.6880 903.91 109.6880 903.91
3 1 5 1 109.6880 903.91 109.6880 903.91
4 1 5 1 99.3110 1065.30 99.3110 1065.30
1 4 7 1 118.5330 365.54 118.5330 365.54
1 5 6 1 118.5330 365.54 118.5330 365.54

[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
2 1 4 7 9 0.00 -12.3261 1 0.00 -12.3261 1
2 1 4 7 9 180.00 -6.9705 2 180.00 -6.9705 2
2 1 4 7 9 0.00 0.6067 3 0.00 0.6067 3
2 1 5 6 9 0.00 -12.3261 1 0.00 -12.3261 1
2 1 5 6 9 180.00 -6.9705 2 180.00 -6.9705 2
2 1 5 6 9 0.00 0.6067 3 0.00 0.6067 3
3 1 4 7 9 0.00 -12.3261 1 0.00 -12.3261 1
3 1 4 7 9 180.00 -6.9705 2 180.00 -6.9705 2
3 1 4 7 9 0.00 0.6067 3 0.00 0.6067 3
3 1 5 6 9 0.00 -12.3261 1 0.00 -12.3261 1
3 1 5 6 9 180.00 -6.9705 2 180.00 -6.9705 2
3 1 5 6 9 0.00 0.6067 3 0.00 0.6067 3
4 1 5 6 9 0.00 -6.7153 1 0.00 -6.7153 1
4 1 5 6 9 180.00 -15.9452 2 180.00 -15.9452 2
4 1 5 6 9 0.00 2.2259 3 0.00 2.2259 3
5 1 4 7 9 0.00 -6.7153 1 0.00 -6.7153 1
5 1 4 7 9 180.00 -15.9452 2 180.00 -15.9452 2
5 1 4 7 9 0.00 2.2259 3 0.00 2.2259 3

[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 4 5 2 2 0.00 0.0000 0.00 0.0000
1 2 5 3 2 0.00 0.0000 0.00 0.0000

#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
…
#endif

receptor.itp

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CB 6 12.0110 0.0 A 0.355005 0.292880
O=C 8 15.9994 0.0 A 0.302905 0.502080
CE4R 6 12.0110 0.0 A 0.370614 0.284512
C=O 6 12.0110 0.0 A 0.356359 0.460240
NC=C 7 14.0067 0.0 A 0.329632 0.836800
HNCO 1 1.0079 0.0 A 0.040001 0.192464
CR 6 12.0110 0.0 A 0.387541 0.230120
HCMM 1 1.0079 0.0 A 0.235197 0.092048
NC=O 7 14.0067 0.0 A 0.329632 0.836800

[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
O=C CB 1 0.302228 0.383470
O=C O=C 1 0.249452 0.502080
O=C CE4R 1 0.310033 0.377952
O=C C=O 1 0.302905 0.480705
O=C NC=C 1 0.289542 0.648182
O=C HNCO 1 0.144726 0.310857
O=C CR 1 0.293997 0.144938
O=C HCMM 1 0.242324 0.214978
O=C NC=O 1 0.289542 0.648182
CR CB 1 0.346773 0.110698
CR CE4R 1 0.354578 0.109105
CR C=O 1 0.347450 0.138768
CR NC=C 1 0.334087 0.187114
CR HNCO 1 0.189271 0.089737
CR CR 1 0.338541 0.041840
CR HCMM 1 0.286869 0.062059
CR NC=O 1 0.334087 0.187114

[ moleculetype ]
; Name nrexcl
LIG 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CB 1 LIG C10 1 -0.1435 12.0110
2 CB 1 LIG C11 2 -0.1500 12.0110
3 CB 1 LIG C12 3 -0.1500 12.0110
4 CB 1 LIG C13 4 -0.1500 12.0110
5 CB 1 LIG C14 5 -0.1500 12.0110
6 CB 1 LIG C15 6 -0.1500 12.0110
7 CB 1 LIG C16 7 -0.1435 12.0110
8 CB 1 LIG C17 8 -0.1500 12.0110
9 CB 1 LIG C18 9 -0.1500 12.0110
10 CB 1 LIG C19 10 -0.1500 12.0110
11 CB 1 LIG C20 11 -0.1500 12.0110
12 CB 1 LIG C21 12 -0.1500 12.0110
13 O=C 1 LIG O 13 -0.5700 15.9994
14 O=C 1 LIG O1 14 -0.5700 15.9994
15 CE4R 1 LIG C 15 0.0270 12.0110
16 CE4R 1 LIG C1 16 0.0270 12.0110
17 C=O 1 LIG C2 17 0.6410 12.0110
18 C=O 1 LIG C3 18 0.6410 12.0110
19 NC=C 1 LIG N 19 -0.8671 14.0067
20 NC=C 1 LIG N1 20 -0.8671 14.0067
21 HNCO 1 LIG H 21 0.4000 1.0079
22 HNCO 1 LIG H1 22 0.4000 1.0079
23 CR 1 LIG C4 23 0.4301 12.0110
24 CR 1 LIG C5 24 0.3691 12.0110
25 HCMM 1 LIG H2 25 0.0000 1.0079
26 HCMM 1 LIG H3 26 0.0000 1.0079
27 HCMM 1 LIG H4 27 0.0000 1.0079
28 C=O 1 LIG C6 28 0.5690 12.0110
29 CR 1 LIG C7 29 0.3001 12.0110
30 O=C 1 LIG O2 30 -0.5700 15.9994
31 NC=O 1 LIG N2 31 -0.7301 14.0067
32 HNCO 1 LIG H5 32 0.3700 1.0079
33 CR 1 LIG C8 33 0.1435 12.0110
34 CR 1 LIG C9 34 0.1435 12.0110
35 HCMM 1 LIG H6 35 0.0000 1.0079
36 HCMM 1 LIG H7 36 0.0000 1.0079
37 HCMM 1 LIG H8 37 0.0000 1.0079
38 HCMM 1 LIG H9 38 0.0000 1.0079
39 HCMM 1 LIG H10 39 0.1500 1.0079
40 HCMM 1 LIG H11 40 0.1500 1.0079
41 HCMM 1 LIG H12 41 0.1500 1.0079
42 HCMM 1 LIG H13 42 0.1500 1.0079
43 HCMM 1 LIG H14 43 0.1500 1.0079
44 HCMM 1 LIG H15 44 0.1500 1.0079
45 HCMM 1 LIG H16 45 0.1500 1.0079
46 HCMM 1 LIG H17 46 0.1500 1.0079
47 HCMM 1 LIG H18 47 0.1500 1.0079
48 HCMM 1 LIG H19 48 0.1500 1.0079
49 HCMM 1 LIG H20 49 0.0000 1.0079
50 C=O 1 LIG C22 50 0.5690 12.0110
51 O=C 1 LIG O3 51 -0.5700 15.9994
52 CR 1 LIG C23 52 0.0610 12.0110
53 HCMM 1 LIG H21 53 0.0000 1.0079
54 HCMM 1 LIG H22 54 0.0000 1.0079
55 HCMM 1 LIG H23 55 0.0000 1.0079
56 NC=O 1 LIG N3 56 -0.7301 14.0067
57 HNCO 1 LIG H24 57 0.3700 1.0079
58 CR 1 LIG C24 58 0.3001 12.0110
59 HCMM 1 LIG H25 59 0.0000 1.0079
60 HCMM 1 LIG H26 60 0.0000 1.0079
61 HCMM 1 LIG H27 61 -0.0000 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
41 4 1 0.10840 319534.6 0.10840 319534.6
…

[ pairs ]
; ai aj fu
1 6 1
1 41 1
…

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 119.9770 402.88 119.9770 402.88
…

[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
1 2 4 6 9 180.00 14.6440 2 180.00 14.6440 2
…

[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 3 34 2 2 0.00 24.0915 0.00 24.0915
…

#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
…
#endif

7

[quote=“juhidutta10, post:6, topic:3859”]
I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each molecule are given below. Kindly help me out. I am new to Gromacs. Also, I want to mention, I have tried all of your solutions, mentioned in the discussion. But nothing was fruitful.

Fatal error:
Syntax error - File receptor.itp, line 8
Last line read:
‘[ atomtypes ] ’
Invalid order for directive atomtypes’

My topol.top file looks like below:

; Include forcefield parameters
#include “charmm27.ff/forcefield.itp”

; Include drg topology
#include “H2PO4.itp”

; Include lig topolgy
#include “receptor.itp”

; 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
System in water

[ molecules ]
; Compound #mols
LIG 1
DRG 1
SOL 6436

The two .itp files mentioned for those two molecules are as follows:

H2PO4.itp

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
PO4 15 30.9738 0.0 A 0.383086 2.447640
O2CM 8 15.9994 0.0 A 0.302905 0.502080
OR 8 15.9994 0.0 A 0.315378 0.636386
HOCO 1 1.0079 0.0 A 0.040001 0.192464

[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS

[ moleculetype ]
; Name nrexcl
DRG 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 PO4 1 DRG P 1 1.7089 30.9738
2 O2CM 1 DRG O 2 -0.9718 15.9994
3 O2CM 1 DRG O1 3 -0.8613 15.9994
4 OR 1 DRG O2 4 -0.8821 15.9994
5 OR 1 DRG O3 5 -0.8625 15.9994
6 HOCO 1 DRG H 6 0.4341 1.0079
7 HOCO 1 DRG H1 7 0.4347 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
5 6 1 0.09810 445818.6 0.09810 445818.6
5 1 1 0.16300 315740.5 0.16300 315740.5
2 1 1 0.15100 499596.4 0.15100 499596.4
1 3 1 0.15100 499596.4 0.15100 499596.4
1 4 1 0.16300 315740.5 0.16300 315740.5
4 7 1 0.09810 445818.6 0.09810 445818.6

[ pairs ]
; ai aj fu
2 7 1
2 6 1
3 7 1
3 6 1
4 6 1
5 7 1

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 122.8570 751.56 122.8570 751.56
2 1 4 1 109.6880 903.91 109.6880 903.91
2 1 5 1 109.6880 903.91 109.6880 903.91
3 1 4 1 109.6880 903.91 109.6880 903.91
3 1 5 1 109.6880 903.91 109.6880 903.91
4 1 5 1 99.3110 1065.30 99.3110 1065.30
1 4 7 1 118.5330 365.54 118.5330 365.54
1 5 6 1 118.5330 365.54 118.5330 365.54

[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
2 1 4 7 9 0.00 -12.3261 1 0.00 -12.3261 1
2 1 4 7 9 180.00 -6.9705 2 180.00 -6.9705 2
2 1 4 7 9 0.00 0.6067 3 0.00 0.6067 3
2 1 5 6 9 0.00 -12.3261 1 0.00 -12.3261 1
2 1 5 6 9 180.00 -6.9705 2 180.00 -6.9705 2
2 1 5 6 9 0.00 0.6067 3 0.00 0.6067 3
3 1 4 7 9 0.00 -12.3261 1 0.00 -12.3261 1
3 1 4 7 9 180.00 -6.9705 2 180.00 -6.9705 2
3 1 4 7 9 0.00 0.6067 3 0.00 0.6067 3
3 1 5 6 9 0.00 -12.3261 1 0.00 -12.3261 1
3 1 5 6 9 180.00 -6.9705 2 180.00 -6.9705 2
3 1 5 6 9 0.00 0.6067 3 0.00 0.6067 3
4 1 5 6 9 0.00 -6.7153 1 0.00 -6.7153 1
4 1 5 6 9 180.00 -15.9452 2 180.00 -15.9452 2
4 1 5 6 9 0.00 2.2259 3 0.00 2.2259 3
5 1 4 7 9 0.00 -6.7153 1 0.00 -6.7153 1
5 1 4 7 9 180.00 -15.9452 2 180.00 -15.9452 2
5 1 4 7 9 0.00 2.2259 3 0.00 2.2259 3

[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 4 5 2 2 0.00 0.0000 0.00 0.0000
1 2 5 3 2 0.00 0.0000 0.00 0.0000

#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
…
#endif

receptor.itp

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CB 6 12.0110 0.0 A 0.355005 0.292880
O=C 8 15.9994 0.0 A 0.302905 0.502080
CE4R 6 12.0110 0.0 A 0.370614 0.284512
C=O 6 12.0110 0.0 A 0.356359 0.460240
NC=C 7 14.0067 0.0 A 0.329632 0.836800
HNCO 1 1.0079 0.0 A 0.040001 0.192464
CR 6 12.0110 0.0 A 0.387541 0.230120
HCMM 1 1.0079 0.0 A 0.235197 0.092048
NC=O 7 14.0067 0.0 A 0.329632 0.836800

[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
O=C CB 1 0.302228 0.383470
O=C O=C 1 0.249452 0.502080
O=C CE4R 1 0.310033 0.377952
O=C C=O 1 0.302905 0.480705
O=C NC=C 1 0.289542 0.648182
O=C HNCO 1 0.144726 0.310857
O=C CR 1 0.293997 0.144938
O=C HCMM 1 0.242324 0.214978
O=C NC=O 1 0.289542 0.648182
CR CB 1 0.346773 0.110698
CR CE4R 1 0.354578 0.109105
CR C=O 1 0.347450 0.138768
CR NC=C 1 0.334087 0.187114
CR HNCO 1 0.189271 0.089737
CR CR 1 0.338541 0.041840
CR HCMM 1 0.286869 0.062059
CR NC=O 1 0.334087 0.187114

[ moleculetype ]
; Name nrexcl
LIG 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CB 1 LIG C10 1 -0.1435 12.0110
2 CB 1 LIG C11 2 -0.1500 12.0110
3 CB 1 LIG C12 3 -0.1500 12.0110
4 CB 1 LIG C13 4 -0.1500 12.0110
5 CB 1 LIG C14 5 -0.1500 12.0110
6 CB 1 LIG C15 6 -0.1500 12.0110
7 CB 1 LIG C16 7 -0.1435 12.0110
8 CB 1 LIG C17 8 -0.1500 12.0110
9 CB 1 LIG C18 9 -0.1500 12.0110
10 CB 1 LIG C19 10 -0.1500 12.0110
11 CB 1 LIG C20 11 -0.1500 12.0110
12 CB 1 LIG C21 12 -0.1500 12.0110
13 O=C 1 LIG O 13 -0.5700 15.9994
14 O=C 1 LIG O1 14 -0.5700 15.9994
15 CE4R 1 LIG C 15 0.0270 12.0110
16 CE4R 1 LIG C1 16 0.0270 12.0110
17 C=O 1 LIG C2 17 0.6410 12.0110
18 C=O 1 LIG C3 18 0.6410 12.0110
19 NC=C 1 LIG N 19 -0.8671 14.0067
20 NC=C 1 LIG N1 20 -0.8671 14.0067
21 HNCO 1 LIG H 21 0.4000 1.0079
22 HNCO 1 LIG H1 22 0.4000 1.0079
23 CR 1 LIG C4 23 0.4301 12.0110
24 CR 1 LIG C5 24 0.3691 12.0110
25 HCMM 1 LIG H2 25 0.0000 1.0079
26 HCMM 1 LIG H3 26 0.0000 1.0079
27 HCMM 1 LIG H4 27 0.0000 1.0079
28 C=O 1 LIG C6 28 0.5690 12.0110
29 CR 1 LIG C7 29 0.3001 12.0110
30 O=C 1 LIG O2 30 -0.5700 15.9994
31 NC=O 1 LIG N2 31 -0.7301 14.0067
32 HNCO 1 LIG H5 32 0.3700 1.0079
33 CR 1 LIG C8 33 0.1435 12.0110
34 CR 1 LIG C9 34 0.1435 12.0110
35 HCMM 1 LIG H6 35 0.0000 1.0079
36 HCMM 1 LIG H7 36 0.0000 1.0079
37 HCMM 1 LIG H8 37 0.0000 1.0079
38 HCMM 1 LIG H9 38 0.0000 1.0079
39 HCMM 1 LIG H10 39 0.1500 1.0079
40 HCMM 1 LIG H11 40 0.1500 1.0079
41 HCMM 1 LIG H12 41 0.1500 1.0079
42 HCMM 1 LIG H13 42 0.1500 1.0079
43 HCMM 1 LIG H14 43 0.1500 1.0079
44 HCMM 1 LIG H15 44 0.1500 1.0079
45 HCMM 1 LIG H16 45 0.1500 1.0079
46 HCMM 1 LIG H17 46 0.1500 1.0079
47 HCMM 1 LIG H18 47 0.1500 1.0079
48 HCMM 1 LIG H19 48 0.1500 1.0079
49 HCMM 1 LIG H20 49 0.0000 1.0079
50 C=O 1 LIG C22 50 0.5690 12.0110
51 O=C 1 LIG O3 51 -0.5700 15.9994
52 CR 1 LIG C23 52 0.0610 12.0110
53 HCMM 1 LIG H21 53 0.0000 1.0079
54 HCMM 1 LIG H22 54 0.0000 1.0079
55 HCMM 1 LIG H23 55 0.0000 1.0079
56 NC=O 1 LIG N3 56 -0.7301 14.0067
57 HNCO 1 LIG H24 57 0.3700 1.0079
58 CR 1 LIG C24 58 0.3001 12.0110
59 HCMM 1 LIG H25 59 0.0000 1.0079
60 HCMM 1 LIG H26 60 0.0000 1.0079
61 HCMM 1 LIG H27 61 -0.0000 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
41 4 1 0.10840 319534.6 0.10840 319534.6
…

[ pairs ]
; ai aj fu
1 6 1
1 41 1
…

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 119.9770 402.88 119.9770 402.88
…

[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
1 2 4 6 9 180.00 14.6440 2 180.00 14.6440 2
…

[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 3 34 2 2 0.00 24.0915 0.00 24.0915
…

#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
…
#endif

8

Hey dear friend，according to your first issue about mismatching coordinate and topology files，I got the same error. I appreciate knowing your answer.