GROMACS version:2021.5
GROMACS modification: Yes/No
Here post your question I am trying to do this tutorial Protein-Ligand Complex
I followed it exactly but i used SwissParam https://www.swissparam.ch/ for generating the itp and par files.
It went well untill i got to the add ions step. When i run
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
a long list of errors like
ERROR 44 [file jz4.prm, line 306]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
appears and at the end it says
Fatal error:
Syntax error - File jz4_-_Copy.itp, line 7
Last line read:
'[ atomtypes ] ’
Invalid order for directive atomtypes
this also happens when using the .par file generated by SwissParam
I added the include ligand and include ligand parameters in the right places in the topol file
Help
Here is the ITP file
; ----
; Built itp for jz4_-_Copy.mol2
; by user vzoete Sun Oct 23 09:56:58 UTC 2022
; ----
;
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CB 6 12.0110 0.0 A 0.355005 0.292880
CR 6 12.0110 0.0 A 0.387541 0.230120
OR 8 15.9994 0.0 A 0.315378 0.636386
HCMM 1 1.0079 0.0 A 0.235197 0.092048
HOCC 1 1.0079 0.0 A 0.040001 0.192464
[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CR CB 1 0.346773 0.110698
CR CR 1 0.338541 0.041840
CR OR 1 0.326960 0.163176
CR HCMM 1 0.286869 0.062059
CR HOCC 1 0.189271 0.089737
[ moleculetype ]
; Name nrexcl
jz4_-_Copy 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CB 1 LIG C7 1 -0.1500 12.0110
2 CB 1 LIG C8 2 -0.1500 12.0110
3 CB 1 LIG C9 3 -0.1500 12.0110
4 CB 1 LIG C10 4 0.0825 12.0110
5 CB 1 LIG C11 5 -0.1500 12.0110
6 CB 1 LIG C12 6 -0.1435 12.0110
7 CR 1 LIG C4 7 0.0000 12.0110
8 CR 1 LIG C13 8 0.1435 12.0110
9 CR 1 LIG C14 9 0.0000 12.0110
10 OR 1 LIG OAB 10 -0.5325 15.9994
11 HCMM 1 LIG H 11 0.0000 1.0079
12 HCMM 1 LIG H1 12 0.0000 1.0079
13 HCMM 1 LIG H2 13 0.0000 1.0079
14 HCMM 1 LIG H3 14 0.1500 1.0079
15 HCMM 1 LIG H4 15 0.1500 1.0079
16 HCMM 1 LIG H5 16 0.1500 1.0079
17 HCMM 1 LIG H6 17 0.1500 1.0079
18 HCMM 1 LIG H7 18 0.0000 1.0079
19 HCMM 1 LIG H8 19 0.0000 1.0079
20 HCMM 1 LIG H9 20 0.0000 1.0079
21 HCMM 1 LIG H10 21 0.0000 1.0079
22 HOCC 1 LIG H11 22 0.4500 1.0079
[ bonds ]
; ai aj fu b0 kb, b0 kb
7 9 1 0.15080 256422.3 0.15080 256422.3
7 11 1 0.10930 287014.9 0.10930 287014.9
7 12 1 0.10930 287014.9 0.10930 287014.9
7 13 1 0.10930 287014.9 0.10930 287014.9
1 2 1 0.13740 335613.7 0.13740 335613.7
1 5 1 0.13740 335613.7 0.13740 335613.7
1 14 1 0.10840 319534.6 0.10840 319534.6
2 3 1 0.13740 335613.7 0.13740 335613.7
2 15 1 0.10840 319534.6 0.10840 319534.6
3 4 1 0.13740 335613.7 0.13740 335613.7
3 16 1 0.10840 319534.6 0.10840 319534.6
4 6 1 0.13740 335613.7 0.13740 335613.7
4 10 1 0.13760 338083.1 0.13760 338083.1
5 6 1 0.13740 335613.7 0.13740 335613.7
5 17 1 0.10840 319534.6 0.10840 319534.6
6 8 1 0.14860 298517.5 0.14860 298517.5
8 9 1 0.15080 256422.3 0.15080 256422.3
8 18 1 0.10930 287014.9 0.10930 287014.9
8 19 1 0.10930 287014.9 0.10930 287014.9
9 20 1 0.10930 287014.9 0.10930 287014.9
9 21 1 0.10930 287014.9 0.10930 287014.9
10 22 1 0.09730 472074.9 0.09730 472074.9
[ pairs ]
; ai aj fu
1 4 1
1 16 1
1 8 1
2 6 1
2 17 1
2 10 1
3 5 1
3 14 1
3 8 1
3 22 1
4 15 1
4 17 1
4 9 1
4 18 1
4 19 1
5 15 1
5 10 1
5 9 1
5 18 1
5 19 1
6 16 1
6 22 1
6 14 1
6 7 1
6 20 1
6 21 1
7 18 1
7 19 1
8 10 1
8 17 1
8 11 1
8 12 1
8 13 1
10 16 1
11 20 1
11 21 1
12 20 1
12 21 1
13 20 1
13 21 1
14 15 1
14 17 1
15 16 1
18 20 1
18 21 1
19 20 1
19 21 1
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 5 1 119.9770 402.88 119.9770 402.88
2 1 14 1 120.5710 339.05 120.5710 339.05
5 1 14 1 120.5710 339.05 120.5710 339.05
1 2 3 1 119.9770 402.88 119.9770 402.88
1 2 15 1 120.5710 339.05 120.5710 339.05
3 2 15 1 120.5710 339.05 120.5710 339.05
2 3 4 1 119.9770 402.88 119.9770 402.88
2 3 16 1 120.5710 339.05 120.5710 339.05
4 3 16 1 120.5710 339.05 120.5710 339.05
3 4 6 1 119.9770 402.88 119.9770 402.88
3 4 10 1 116.4950 582.94 116.4950 582.94
6 4 10 1 116.4950 582.94 116.4950 582.94
1 5 6 1 119.9770 402.88 119.9770 402.88
1 5 17 1 120.5710 339.05 120.5710 339.05
6 5 17 1 120.5710 339.05 120.5710 339.05
4 6 5 1 119.9770 402.88 119.9770 402.88
4 6 8 1 120.4190 483.57 120.4190 483.57
5 6 8 1 120.4190 483.57 120.4190 483.57
9 7 11 1 110.5490 383.00 110.5490 383.00
9 7 12 1 110.5490 383.00 110.5490 383.00
9 7 13 1 110.5490 383.00 110.5490 383.00
11 7 12 1 108.8360 310.74 108.8360 310.74
11 7 13 1 108.8360 310.74 108.8360 310.74
12 7 13 1 108.8360 310.74 108.8360 310.74
6 8 9 1 108.6170 455.27 108.6170 455.27
6 8 18 1 109.4910 377.58 109.4910 377.58
6 8 19 1 109.4910 377.58 109.4910 377.58
9 8 18 1 110.5490 383.00 110.5490 383.00
9 8 19 1 110.5490 383.00 110.5490 383.00
18 8 19 1 108.8360 310.74 108.8360 310.74
7 9 8 1 109.6080 512.48 109.6080 512.48
7 9 20 1 110.5490 383.00 110.5490 383.00
7 9 21 1 110.5490 383.00 110.5490 383.00
8 9 20 1 110.5490 383.00 110.5490 383.00
8 9 21 1 110.5490 383.00 110.5490 383.00
20 9 21 1 108.8360 310.74 108.8360 310.74
4 10 22 1 105.4090 437.20 105.4090 437.20
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
1 2 3 4 9 180.00 14.6440 2 180.00 14.6440 2
1 2 3 16 9 180.00 14.6440 2 180.00 14.6440 2
1 5 6 4 9 180.00 14.6440 2 180.00 14.6440 2
1 5 6 8 9 180.00 14.6440 2 180.00 14.6440 2
2 1 5 6 9 180.00 14.6440 2 180.00 14.6440 2
2 1 5 17 9 180.00 14.6440 2 180.00 14.6440 2
2 3 4 6 9 180.00 14.6440 2 180.00 14.6440 2
2 3 4 10 9 180.00 14.6440 2 180.00 14.6440 2
3 2 1 5 9 180.00 14.6440 2 180.00 14.6440 2
3 2 1 14 9 180.00 14.6440 2 180.00 14.6440 2
3 4 6 5 9 180.00 14.6440 2 180.00 14.6440 2
3 4 6 8 9 180.00 14.6440 2 180.00 14.6440 2
3 4 10 22 9 180.00 5.8618 2 180.00 5.8618 2
4 3 2 15 9 180.00 14.6440 2 180.00 14.6440 2
4 6 5 17 9 180.00 14.6440 2 180.00 14.6440 2
4 6 8 9 9 180.00 0.9414 2 180.00 0.9414 2
4 6 8 18 9 180.00 -0.8786 2 180.00 -0.8786 2
4 6 8 18 9 0.00 0.8201 3 0.00 0.8201 3
4 6 8 19 9 180.00 -0.8786 2 180.00 -0.8786 2
4 6 8 19 9 0.00 0.8201 3 0.00 0.8201 3
5 1 2 15 9 180.00 14.6440 2 180.00 14.6440 2
5 6 4 10 9 180.00 14.6440 2 180.00 14.6440 2
5 6 8 9 9 180.00 0.9414 2 180.00 0.9414 2
5 6 8 18 9 180.00 -0.8786 2 180.00 -0.8786 2
5 6 8 18 9 0.00 0.8201 3 0.00 0.8201 3
5 6 8 19 9 180.00 -0.8786 2 180.00 -0.8786 2
5 6 8 19 9 0.00 0.8201 3 0.00 0.8201 3
6 4 3 16 9 180.00 14.6440 2 180.00 14.6440 2
6 4 10 22 9 180.00 5.8618 2 180.00 5.8618 2
6 5 1 14 9 180.00 14.6440 2 180.00 14.6440 2
6 8 9 7 9 0.00 0.6276 3 0.00 0.6276 3
6 8 9 20 9 0.00 0.8159 3 0.00 0.8159 3
6 8 9 21 9 0.00 0.8159 3 0.00 0.8159 3
7 9 8 18 9 0.00 1.3389 1 0.00 1.3389 1
7 9 8 18 9 180.00 -1.3180 2 180.00 -1.3180 2
7 9 8 18 9 0.00 0.5523 3 0.00 0.5523 3
7 9 8 19 9 0.00 1.3389 1 0.00 1.3389 1
7 9 8 19 9 180.00 -1.3180 2 180.00 -1.3180 2
7 9 8 19 9 0.00 0.5523 3 0.00 0.5523 3
8 6 4 10 9 180.00 14.6440 2 180.00 14.6440 2
8 6 5 17 9 180.00 14.6440 2 180.00 14.6440 2
8 9 7 11 9 0.00 1.3389 1 0.00 1.3389 1
8 9 7 11 9 180.00 -1.3180 2 180.00 -1.3180 2
8 9 7 11 9 0.00 0.5523 3 0.00 0.5523 3
8 9 7 12 9 0.00 1.3389 1 0.00 1.3389 1
8 9 7 12 9 180.00 -1.3180 2 180.00 -1.3180 2
8 9 7 12 9 0.00 0.5523 3 0.00 0.5523 3
8 9 7 13 9 0.00 1.3389 1 0.00 1.3389 1
8 9 7 13 9 180.00 -1.3180 2 180.00 -1.3180 2
8 9 7 13 9 0.00 0.5523 3 0.00 0.5523 3
10 4 3 16 9 180.00 14.6440 2 180.00 14.6440 2
11 7 9 20 9 0.00 0.5941 1 0.00 0.5941 1
11 7 9 20 9 180.00 -2.8995 2 180.00 -2.8995 2
11 7 9 20 9 0.00 0.6569 3 0.00 0.6569 3
11 7 9 21 9 0.00 0.5941 1 0.00 0.5941 1
11 7 9 21 9 180.00 -2.8995 2 180.00 -2.8995 2
11 7 9 21 9 0.00 0.6569 3 0.00 0.6569 3
12 7 9 20 9 0.00 0.5941 1 0.00 0.5941 1
12 7 9 20 9 180.00 -2.8995 2 180.00 -2.8995 2
12 7 9 20 9 0.00 0.6569 3 0.00 0.6569 3
12 7 9 21 9 0.00 0.5941 1 0.00 0.5941 1
12 7 9 21 9 180.00 -2.8995 2 180.00 -2.8995 2
12 7 9 21 9 0.00 0.6569 3 0.00 0.6569 3
13 7 9 20 9 0.00 0.5941 1 0.00 0.5941 1
13 7 9 20 9 180.00 -2.8995 2 180.00 -2.8995 2
13 7 9 20 9 0.00 0.6569 3 0.00 0.6569 3
13 7 9 21 9 0.00 0.5941 1 0.00 0.5941 1
13 7 9 21 9 180.00 -2.8995 2 180.00 -2.8995 2
13 7 9 21 9 0.00 0.6569 3 0.00 0.6569 3
14 1 2 15 9 180.00 14.6440 2 180.00 14.6440 2
14 1 5 17 9 180.00 14.6440 2 180.00 14.6440 2
15 2 3 16 9 180.00 14.6440 2 180.00 14.6440 2
18 8 9 20 9 0.00 0.5941 1 0.00 0.5941 1
18 8 9 20 9 180.00 -2.8995 2 180.00 -2.8995 2
18 8 9 20 9 0.00 0.6569 3 0.00 0.6569 3
18 8 9 21 9 0.00 0.5941 1 0.00 0.5941 1
18 8 9 21 9 180.00 -2.8995 2 180.00 -2.8995 2
18 8 9 21 9 0.00 0.6569 3 0.00 0.6569 3
19 8 9 20 9 0.00 0.5941 1 0.00 0.5941 1
19 8 9 20 9 180.00 -2.8995 2 180.00 -2.8995 2
19 8 9 20 9 0.00 0.6569 3 0.00 0.6569 3
19 8 9 21 9 0.00 0.5941 1 0.00 0.5941 1
19 8 9 21 9 180.00 -2.8995 2 180.00 -2.8995 2
19 8 9 21 9 0.00 0.6569 3 0.00 0.6569 3
[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 2 5 14 2 0.00 9.0291 0.00 9.0291
2 3 1 15 2 0.00 9.0291 0.00 9.0291
3 4 2 16 2 0.00 9.0291 0.00 9.0291
4 6 3 10 2 0.00 28.9031 0.00 28.9031
6 5 4 8 2 0.00 24.0915 0.00 24.0915
8 9 6 18 2 0.00 0.0000 0.00 0.0000
8 9 6 19 2 0.00 0.0000 0.00 0.0000
9 7 8 20 2 0.00 0.0000 0.00 0.0000
9 7 8 21 2 0.00 0.0000 0.00 0.0000
7 11 9 12 2 0.00 0.0000 0.00 0.0000
7 11 9 13 2 0.00 0.0000 0.00 0.0000
5 6 1 17 2 0.00 9.0291 0.00 9.0291
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
#endif
topol file:
; :-) GROMACS - gmx pdb2gmx, 2021.5 (-:
;
; Executable: D:\groomax\bin\gmx.exe
; Data prefix: D:\groomax
; Working dir: D:\groomax
; Command line:
; gmx pdb2gmx -f 3htbe.pdb -ignh -ter -o 3HTB.gro
; Force field was read from current directory or a relative path - path added.
;
; Include forcefield parameters
#include “./charmm36-jul2022.ff/forcefield.itp”
; Include ligand parameters
#include “jz4_-_Copy.par”
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 MET rtp MET q +1.0
1 NH3 1 MET N 1 -0.3 14.007
2 HC 1 MET H1 2 0.33 1.008
3 HC 1 MET H2 3 0.33 1.008
.
.
.
2555 2557 2559 2576 2578 1
2576 2578 2580 2598 2600 1
; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif
; Include ligand topology
#include “jz4_-_Copy.itp”
; Include water topology
#include “./charmm36-jul2022.ff/tip3p_original.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 “./charmm36-jul2022.ff/ions.itp”
[ system ]
; Name
2-PROPYLPHENOL IN COMPLEX WITH T4 LYSOZYME L99A/M102Q in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
SOL 10294
If this were true, you would not be getting fatal errors :)
If the ligand .itp file includes new atom types, it must be #included before any [moleculetype] is introduced. If your .prm (or .par) file provides some new parameters, they must be compatible with the parent force field (e.g. the Buckingham vs. LJ issue).
Where and how do i include the atomtypes? Do i add them in the atomtypes atm file in the forcefield folder? Also how do i change the parent force field?
I am very new to this sorry
I cannot make any recommendation about trying to work SwissParam into my tutorial but the principles are the same, in general. Refer to Common errors when using GROMACS — GROMACS 2022.3 documentation for understanding how to solve specific errors, and the topology hierarchy is given in the manual (Topologies — GROMACS 2022.3 documentation).