[gmx-users] how can we include excluded atoms
Anjali Patel
anjalipatel60316 at gmail.com
Wed Aug 7 09:14:37 CEST 2019
Hello user,
i have gone through the manual and according to that all atoms are bonded.
still its showing non-bonded parameters with excluded atoms. due to this
its showing error like this,
Excluding 1 bonded neighbours molecule type 'NP5Q'
Excluding 3 bonded neighbours molecule type 'DRG'
Excluding 2 bonded neighbours molecule type 'SOL'
WARNING 1 [file topol.top, line 60]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Check if molecules in your system
are affected by such issues before proceeding. Further information may be
available at https://redmine.gromacs.org/issues/2884.
Fatal error:
number of coordinates in coordinate file (solv.gro, 3789)
does not match topology (topol.top, 3777)
*topol.top*
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "./gromos54a7.ff/forcefield.itp"
; Include CNT topology
#include "3pb.itp"
; Include LIG_GMX.itp topology
#include "sialic-new.itp"
; Ligand position restraints
#ifdef POSRES_LIG
#include "posre.itp"
#endif
; Include topology for ions
#include "./gromos54a7_atb.ff/spc.itp"
; Include topology for ions
#include "./gromos54a7_atb.ff/ions.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include water topology
;#include "./gromos54a7_atb.ff/tip3p.itp"
[ system ]
; Name
NP5Q in water
[ molecules ]
; Compound #mols
NP5Q 1
DRG 1
SOL 1234
*3pb.itp*
[ moleculetype ]
; Name nrexcl
NP5Q 1
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 H 1 NP5Q H12 1 %% 1.0080
2 OEOpt 1 NP5Q O5 2 %% 15.9994
3 B 1 NP5Q B3 3 %% 10.8110
4 OEOpt 1 NP5Q O6 4 %% 15.9994
5 H 1 NP5Q H11 5 %% 1.0080
6 C 1 NP5Q C17 6 %% 12.0110
7 C 1 NP5Q C16 7 %% 12.0110
8 HC 1 NP5Q H16 8 %% 1.0080
9 C 1 NP5Q C20 9 %% 12.0110
10 HC 1 NP5Q H15 10 %% 1.0080
11 C 1 NP5Q C19 11 %% 12.0110
12 HC 1 NP5Q H14 12 %% 1.0080
13 C 1 NP5Q C15 13 %% 12.0110
14 C 1 NP5Q C18 14 %% 12.0110
15 HC 1 NP5Q H13 15 %% 1.0080
16 C 1 NP5Q C22 16 %% 12.0110
17 C 1 NP5Q C21 17 %% 12.0110
18 CAro 1 NP5Q C10 18 %% 12.0110
19 CAro 1 NP5Q C11 19 %% 12.0110
20 B 1 NP5Q B1 20 %% 10.8110
21 OEOpt 1 NP5Q O1 21 %% 15.9994
22 H 1 NP5Q H2 22 %% 1.0080
23 OEOpt 1 NP5Q O2 23 %% 15.9994
24 H 1 NP5Q H1 24 %% 1.0080
25 CAro 1 NP5Q C12 25 %% 12.0110
26 HC 1 NP5Q H5 26 %% 1.0080
27 CAro 1 NP5Q C9 27 %% 12.0110
28 CAro 1 NP5Q C13 28 %% 12.0110
29 HC 1 NP5Q H6 29 %% 1.0080
30 CAro 1 NP5Q C14 30 %% 12.0110
31 HC 1 NP5Q H7 31 %% 1.0080
32 C 1 NP5Q C8 32 %% 12.0110
33 C 1 NP5Q C7 33 %% 12.0110
34 CAro 1 NP5Q C1 34 %% 12.0110
35 CAro 1 NP5Q C2 35 %% 12.0110
36 HC 1 NP5Q H10 36 %% 1.0080
37 CAro 1 NP5Q C3 37 %% 12.0110
38 B 1 NP5Q B2 38 %% 10.8110
39 OEOpt 1 NP5Q O3 39 %% 15.9994
40 H 1 NP5Q H3 40 %% 1.0080
41 OEOpt 1 NP5Q O4 41 %% 15.9994
42 H 1 NP5Q H4 42 %% 1.0080
43 CAro 1 NP5Q C4 43 %% 12.0110
44 HC 1 NP5Q H17 44 %% 1.0080
45 CAro 1 NP5Q C5 45 %% 12.0110
46 HC 1 NP5Q H9 46 %% 1.0080
47 CAro 1 NP5Q C6 47 %% 12.0110
48 HC 1 NP5Q H8 48 %% 1.0080
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.0971 7.9547e+06
2 3 2 0.1560 3.0819e+06
3 4 2 0.1560 3.0819e+06
3 6 2 0.1640 3.5321e+06
4 5 2 0.0971 7.9547e+06
6 7 2 0.1435 6.1000e+06
6 14 2 0.1390 8.6600e+06
7 8 2 0.1090 1.2300e+07
7 9 2 0.1420 3.2236e+06
9 10 2 0.1090 1.2300e+07
9 11 2 0.1360 1.0200e+07
11 12 2 0.1090 1.2300e+07
11 13 2 0.1300 3.8462e+06
13 14 2 0.1310 1.2528e+07
13 16 2 0.1420 3.2236e+06
14 15 2 0.1110 4.8697e+06
16 17 2 0.1250 1.3400e+07
17 18 2 0.1500 8.3700e+06
18 19 2 0.1420 3.2236e+06
18 30 2 0.1400 8.5400e+06
19 20 2 0.1610 4.8400e+06
19 25 2 0.1390 8.6600e+06
20 21 2 0.1470 8.7100e+06
20 23 2 0.1470 8.7100e+06
21 22 2 0.0971 7.9547e+06
23 24 2 0.0971 7.9547e+06
25 26 2 0.1100 1.2100e+07
25 27 2 0.1430 8.1800e+06
27 28 2 0.1420 3.2236e+06
27 32 2 0.1380 1.1000e+07
28 29 2 0.1070 1.7032e+07
28 30 2 0.1360 1.0200e+07
30 31 2 0.1070 1.7032e+07
32 33 2 0.1180 3.5909e+07
33 34 2 0.1435 6.1000e+06
34 35 2 0.1410 6.5389e+06
34 47 2 0.1430 8.1800e+06
35 36 2 0.1090 1.2300e+07
35 37 2 0.1390 8.6600e+06
37 38 2 0.1600 2.1484e+06
37 43 2 0.1420 3.2236e+06
38 39 2 0.1490 1.4189e+07
38 41 2 0.1490 1.4189e+07
39 40 2 0.0985 8.2455e+07
41 42 2 0.0985 8.2455e+07
43 44 2 0.1090 1.2300e+07
43 45 2 0.1410 6.5389e+06
45 46 2 0.1090 1.2300e+07
45 47 2 0.1390 8.6600e+06
47 48 2 0.1070 1.7032e+07
18 27 2
19 28 2
25 30 2
34 43 2
35 45 2
37 47 2
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 4 1
1 6 1
2 5 1
2 7 1
2 14 1
3 8 1
3 9 1
3 13 1
3 15 1
4 7 1
4 14 1
5 6 1
6 10 1
6 11 1
6 16 1
7 12 1
7 13 1
7 15 1
8 10 1
8 11 1
8 14 1
9 14 1
9 16 1
10 12 1
10 13 1
11 15 1
11 17 1
12 14 1
12 16 1
13 18 1
14 17 1
15 16 1
16 19 1
16 30 1
17 20 1
17 25 1
17 28 1
17 31 1
18 21 1
18 23 1
18 26 1
18 29 1
19 22 1
19 24 1
19 31 1
19 32 1
20 26 1
20 27 1
20 30 1
21 24 1
21 25 1
22 23 1
23 25 1
25 29 1
25 33 1
26 28 1
26 32 1
27 31 1
27 34 1
28 33 1
29 31 1
29 32 1
30 32 1
32 35 1
32 47 1
33 36 1
33 37 1
33 45 1
33 48 1
34 38 1
34 46 1
35 39 1
35 41 1
35 44 1
35 48 1
36 38 1
36 43 1
36 47 1
37 40 1
37 42 1
37 46 1
38 44 1
38 45 1
39 42 1
39 43 1
40 41 1
41 43 1
43 48 1
44 46 1
44 47 1
46 48 1
[ angles ]
; ai aj ak funct angle fc
1 2 3 2 109.50 450.00
2 3 4 2 119.00 2211.40
2 3 6 2 120.00 390.00
4 3 6 2 120.00 390.00
3 4 5 2 109.50 450.00
3 6 7 2 120.00 560.00
3 6 14 2 120.00 560.00
7 6 14 2 120.00 560.00
6 7 8 2 120.00 505.00
6 7 9 2 120.00 560.00
8 7 9 2 120.00 505.00
7 9 10 2 120.00 505.00
7 9 11 2 120.00 560.00
10 9 11 2 120.00 505.00
9 11 12 2 120.00 505.00
9 11 13 2 111.00 530.00
12 11 13 2 126.00 575.00
11 13 14 2 132.00 760.00
11 13 16 2 97.90 16311.89
14 13 16 2 120.00 560.00
6 14 13 2 111.00 530.00
6 14 15 2 126.00 575.00
13 14 15 2 126.00 575.00
13 16 17 2 180.00 500.00
16 17 18 2 180.00 500.00
17 18 19 2 120.00 560.00
17 18 30 2 120.00 560.00
19 18 30 2 120.00 560.00
18 19 20 2 120.00 560.00
18 19 25 2 120.00 560.00
20 19 25 2 120.00 560.00
19 20 21 2 120.00 390.00
19 20 23 2 120.00 390.00
21 20 23 2 118.00 7474.41
20 21 22 2 109.50 450.00
20 23 24 2 109.50 450.00
19 25 26 2 120.00 505.00
19 25 27 2 120.00 560.00
26 25 27 2 120.00 505.00
25 27 28 2 120.00 560.00
25 27 32 2 120.00 560.00
28 27 32 2 126.00 640.00
27 28 29 2 120.00 505.00
27 28 30 2 120.00 560.00
29 28 30 2 120.00 505.00
18 30 28 2 120.00 560.00
18 30 31 2 120.00 505.00
28 30 31 2 120.00 505.00
27 32 33 2 180.00 500.00
32 33 34 2 180.00 500.00
33 34 35 2 120.00 560.00
33 34 47 2 120.00 560.00
35 34 47 2 120.00 560.00
34 35 36 2 120.00 505.00
34 35 37 2 120.00 560.00
36 35 37 2 120.00 505.00
35 37 38 2 120.00 560.00
35 37 43 2 120.00 560.00
38 37 43 2 120.00 560.00
37 38 39 2 119.00 2211.40
37 38 41 2 119.00 2211.40
39 38 41 2 120.00 390.00
38 39 40 2 109.50 450.00
38 41 42 2 109.50 450.00
37 43 44 2 120.00 505.00
37 43 45 2 120.00 560.00
44 43 45 2 120.00 505.00
43 45 46 2 120.00 505.00
43 45 47 2 120.00 560.00
46 45 47 2 120.00 505.00
34 47 45 2 120.00 560.00
34 47 48 2 120.00 505.00
45 47 48 2 120.00 505.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
34 33 35 47 2 0.00 167.36
35 34 36 37 2 0.00 167.36
37 35 38 43 2 0.00 167.36
43 37 44 45 2 0.00 167.36
45 43 46 47 2 0.00 167.36
47 34 45 48 2 0.00 167.36
27 25 28 32 2 0.00 167.36
18 17 19 30 2 0.00 167.36
19 18 20 25 2 0.00 167.36
25 19 26 27 2 0.00 167.36
28 27 29 30 2 0.00 167.36
30 18 28 31 2 0.00 167.36
20 19 21 23 2 0.00 167.36
38 37 39 41 2 0.00 167.36
7 6 8 9 2 0.00 167.36
6 3 7 14 2 0.00 167.36
14 6 13 15 2 0.00 167.36
11 9 12 13 2 0.00 167.36
9 7 10 11 2 0.00 167.36
3 2 4 6 2 0.00 167.36
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
1 2 3 6 1 180.00 5.86 2
2 3 6 7 1 0.00 0.42 2
6 3 4 5 1 180.00 5.86 2
6 7 9 11 1 180.00 5.86 2
7 6 14 13 1 180.00 5.86 2
7 9 11 13 1 180.00 5.86 2
9 11 13 14 1 180.00 5.86 2
11 13 14 6 1 180.00 5.86 2
14 6 7 9 1 180.00 5.86 2
18 19 20 21 1 0.00 0.42 2
18 19 25 27 1 180.00 41.80 2
19 18 30 28 1 180.00 41.80 2
19 20 21 22 1 180.00 5.86 2
19 20 23 24 1 180.00 5.86 2
19 25 27 28 1 180.00 41.80 2
25 27 28 30 1 180.00 41.80 2
27 28 30 18 1 180.00 41.80 2
30 18 19 25 1 180.00 41.80 2
34 35 37 43 1 180.00 41.80 2
35 34 47 45 1 180.00 41.80 2
35 37 38 39 1 0.00 0.42 2
35 37 43 45 1 180.00 41.80 2
37 38 39 40 1 180.00 5.86 2
37 38 41 42 1 180.00 5.86 2
37 43 45 47 1 180.00 41.80 2
43 45 47 34 1 180.00 41.80 2
47 34 35 37 1 180.00 41.80 2
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions
18 27
19 28
25 30
34 43
35 45
37 47
somthing is going wrong or how can i include these atoms in my
calculations?
your help will be appreciated
thank you.
With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002,
Gujarat, India.
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