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?
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
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.
CAR.itp is the ligand.itp
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.
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.
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”
;
; 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
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
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
The ligand [moleculetype] is not named CAR, it is named UNK:
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!