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topol.top
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topol.top
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;
; File 'topol.top' was generated
; By user: spiwokv (1000)
; On host: arabica
; At date: Mon Jul 20 11:45:17 2020
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2019.4 (double precision) (-:
;
; Executable: /software/gromacs2019plumed26/bin/gmx_mpi_d
; Data prefix: /software/gromacs2019plumed26
; Working dir: /home/spiwokv/fgnocvs/acealanme/n1
; Command line:
; gmx_mpi_d pdb2gmx -f AceAla1Nme.pdb -o protein
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ACE rtp ACE q 0.0
1 CT 1 ACE CH3 1 -0.3662 12.01
2 HC 1 ACE HH31 2 0.1123 1.008
3 HC 1 ACE HH32 3 0.1123 1.008
4 HC 1 ACE HH33 4 0.1123 1.008
5 C 1 ACE C 5 0.5972 12.01
6 O 1 ACE O 6 -0.5679 16 ; qtot 0
; residue 2 ALA rtp ALA q 0.0
7 N 2 ALA N 7 -0.4157 14.01
8 H 2 ALA H 8 0.2719 1.008
9 CT 2 ALA CA 9 0.0337 12.01
10 H1 2 ALA HA 10 0.0823 1.008
11 CT 2 ALA CB 11 -0.1825 12.01
12 HC 2 ALA HB1 12 0.0603 1.008
13 HC 2 ALA HB2 13 0.0603 1.008
14 HC 2 ALA HB3 14 0.0603 1.008
15 C 2 ALA C 15 0.5973 12.01
16 O 2 ALA O 16 -0.5679 16 ; qtot 0
; residue 3 NME rtp NME q 0.0
17 N 3 NME N 17 -0.4157 14.01
18 H 3 NME H 18 0.2719 1.008
19 CT 3 NME CH3 19 -0.149 12.01
20 H1 3 NME HH31 20 0.0976 1.008
21 H1 3 NME HH32 21 0.0976 1.008
22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
7 8 1
7 9 1
9 10 1
9 11 1
9 15 1
11 12 1
11 13 1
11 14 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
19 21 1
19 22 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
2 6 1
2 7 1
3 6 1
3 7 1
4 6 1
4 7 1
5 10 1
5 11 1
5 15 1
6 8 1
6 9 1
7 12 1
7 13 1
7 14 1
7 16 1
7 17 1
8 10 1
8 11 1
8 15 1
9 18 1
9 19 1
10 12 1
10 13 1
10 14 1
10 16 1
10 17 1
11 16 1
11 17 1
12 15 1
13 15 1
14 15 1
15 20 1
15 21 1
15 22 1
16 18 1
16 19 1
18 20 1
18 21 1
18 22 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
6 5 7 1
5 7 8 1
5 7 9 1
8 7 9 1
7 9 10 1
7 9 11 1
7 9 15 1
10 9 11 1
10 9 15 1
11 9 15 1
9 11 12 1
9 11 13 1
9 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
9 15 16 1
9 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 9
2 1 5 7 9
3 1 5 6 9
3 1 5 7 9
4 1 5 6 9
4 1 5 7 9
1 5 7 8 9
1 5 7 9 9
6 5 7 8 9
6 5 7 9 9
5 7 9 10 9
5 7 9 11 9
5 7 9 15 9
8 7 9 10 9
8 7 9 11 9
8 7 9 15 9
7 9 11 12 9
7 9 11 13 9
7 9 11 14 9
10 9 11 12 9
10 9 11 13 9
10 9 11 14 9
15 9 11 12 9
15 9 11 13 9
15 9 11 14 9
7 9 15 16 9
7 9 15 17 9
10 9 15 16 9
10 9 15 17 9
11 9 15 16 9
11 9 15 17 9
9 15 17 18 9
9 15 17 19 9
16 15 17 18 9
16 15 17 19 9
15 17 19 20 9
15 17 19 21 9
15 17 19 22 9
18 17 19 20 9
18 17 19 21 9
18 17 19 22 9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
1 7 5 6 4
5 9 7 8 4
9 17 15 16 4
15 19 17 18 4
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber99sb-ildn.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-ildn.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1