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
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; 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?