How do I solve this problem? - Fatal error in Gromacs

Marco91 · January 16, 2022, 6:42pm

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?

jalemkul · January 16, 2022, 6:54pm

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

Marco91 · January 16, 2022, 7:57pm

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.

Marco91 · January 16, 2022, 7:59pm

CAR.itp is the ligand.itp

jalemkul · January 17, 2022, 2:00am

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.

Marco91 · January 17, 2022, 8:44am

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.

jalemkul · January 17, 2022, 10:52am

Please upload the ligand .itp file so we can look at it. This should be the correct sequence of statements that fixes the issue:

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

; Include Ligand topology
#include “CAR.itp”

Marco91 · January 17, 2022, 11:39am

;
; 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 8 7 6 2 12 11 7 8 12 11 7 6 4 3 2 1 4 5 1 2 14 12 11 7 15 14 12 11 15 14 12 13 7 6 2 1 7 6 2 3 6 2 1 5 6 2 3 4 24 11 12 14 24 11 12 13 24 11 7 8 24 11 7 6 24 11 7 22 18 3 4 5 18 3 2 6 18 3 2 1 30 16 15 14 29 16 15 14 30 16 15 28 30 16 15 27 29 16 15 28 29 16 15 27 19 4 3 2 19 4 3 18 19 4 5 1 17 1 2 6 17 1 2 3 17 1 5 4 26 14 12 11 25 14 12 11 26 14 12 13 22 7 8 9 25 14 12 13 22 7 8 10 27 15 14 12 20 6 7 8 21 6 7 8 28 15 14 12 22 7 6 2 28 15 14 26 27 15 14 25 22 7 6 21 27 15 14 26 22 7 6 20 28 15 14 25 20 6 7 11 21 6 7 11 25 14 15 16 26 14 15 16 20 6 2 1 21 6 2 1 20 6 2 3 21 6 2 3 22 7 11 12 23 10 8 7 23 10 8 9 11 7 8 9 11 7 8 10 11 7 6 2 3 4 5 1 5 4 3 2 5 1 2 3 16 15 14 12 9 8 7 6 13 12 11 7 10 8 7 6 ak al funct c0 c1 c2 c3 c4 c5
3 -4.960 6.286 1.310 -2.636 -0.000 0.000
3 -2.910 -0.387 -3.816 7.113 -0.000 0.000
3 1.933 0.000 -1.933 -0.000 -0.000 0.000
3 20.920 0.000 -20.920 -0.000 -0.000 0.000
3 30.334 0.000 -30.334 -0.000 -0.000 0.000
3 30.288 -4.812 -25.476 -0.000 -0.000 0.000
3 0.734 -9.985 -0.791 10.042 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 1.046 -3.556 2.510 -0.000 -0.000 0.000
3 9.079 0.000 -9.079 -0.000 -0.000 0.000
3 20.920 0.000 -20.920 -0.000 -0.000 0.000
3 20.502 0.000 -20.502 -0.000 -0.000 0.000
3 20.502 0.000 -20.502 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 20.920 0.000 -20.920 -0.000 -0.000 0.000
3 20.920 0.000 -20.920 -0.000 -0.000 0.000
3 20.920 0.000 -20.920 -0.000 -0.000 0.000
3 -1.268 3.021 1.745 -3.498 -0.000 0.000
3 -1.268 3.021 1.745 -3.498 -0.000 0.000
3 0.837 2.510 0.000 -3.347 -0.000 0.000
3 0.837 2.510 0.000 -3.347 -0.000 0.000
3 0.837 2.510 0.000 -3.347 -0.000 0.000
3 0.837 2.510 0.000 -3.347 -0.000 0.000
3 41.840 0.000 -41.840 -0.000 -0.000 0.000
3 41.840 0.000 -41.840 -0.000 -0.000 0.000
3 41.840 0.000 -41.840 -0.000 -0.000 0.000
3 44.978 0.000 -44.978 -0.000 -0.000 0.000
3 44.978 0.000 -44.978 -0.000 -0.000 0.000
3 30.334 0.000 -30.334 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 -0.209 -0.628 0.000 0.837 -0.000 0.000
3 -0.209 -0.628 0.000 0.837 -0.000 0.000
3 -0.209 -0.628 0.000 0.837 -0.000 0.000
3 -0.209 -0.628 0.000 0.837 -0.000 0.000
3 0.967 2.900 0.000 -3.866 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.628 1.883 0.000 -2.510 -0.000 0.000
3 0.971 2.912 0.000 -3.883 -0.000 0.000
3 0.971 2.912 0.000 -3.883 -0.000 0.000
3 -4.096 5.088 2.966 -3.958 -0.000 0.000
3 -4.096 5.088 2.966 -3.958 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 26.150 -3.138 -23.012 -0.000 -0.000 0.000
3 23.012 0.000 -23.012 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 -0.766 2.707 4.025 -5.966 -0.000 0.000
3 41.840 0.000 -41.840 -0.000 -0.000 0.000
3 41.840 0.000 -41.840 -0.000 -0.000 0.000
3 30.334 0.000 -30.334 -0.000 -0.000 0.000
3 3.335 -1.552 2.820 -4.602 -0.000 0.000
3 0.000 0.000 0.000 -0.000 -0.000 0.000
3 25.476 0.000 -25.476 -0.000 -0.000 0.000
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

Marco91 · January 17, 2022, 12:10pm

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

Marco91 · January 17, 2022, 12:11pm

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

jalemkul · January 17, 2022, 1:05pm

The ligand [moleculetype] is not named CAR, it is named UNK:

Marco91 · January 17, 2022, 3:45pm

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!

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How do I solve this problem? - Fatal error in Gromacs

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