[gmx-users] invalid pairstype 180
Monoj Mon Kalita
mon.123chem at gmail.com
Thu Mar 28 18:14:33 CET 2013
Dear GMX-Users
I have a problem while trying to insert a drug molecule into my simulation.
I have the topology file generated from the ATB-server. And accordingly I
have edited the aminoacid.rtp & ffbonded.itp file. I have transcribed the
forcefield parameters into GROMOS96 format. here is my .itp file for that
molecule. My problem is that after doing all the things when i tried to do
sd minimization then i got the error message like
*Program grompp, VERSION 4.5.5*
*Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/topdirs.c, line: 107*
*
*
*Fatal error:*
*Invalid pairs type 180*
*For more information and tips for troubleshooting, please check the GROMACS
*
*website at http://www.gromacs.org/Documentation/Errors*
What may be the reason ? And when i studied through the .itp file then i
have found the 1-4 interactions in the [ pairs ] section followed by the
excluded 1-4 interactions. Now, my other question is that should I address
these 1-4 interactions in the ffnonbonded.itp file ! Looking forward for
kind response.
[ moleculetype ]
; Name nrexcl
_NW5 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 CH3 1 _NW5 C14 1 -0.000 15.0350 ; 0.000
2 C 1 _NW5 C8 2 -0.217 12.0110
3 HC 1 _NW5 H1 2 0.138 1.0080
4 C 1 _NW5 C11 2 -0.111 12.0110
5 C 1 _NW5 C15 2 0.717 12.0110
6 O 1 _NW5 O1 2 -0.580 15.9994
7 N 1 _NW5 N2 2 -0.663 14.0067
8 H 1 _NW5 H8 2 0.372 1.0080
9 C 1 _NW5 C16 2 0.785 12.0110
10 NT 1 _NW5 N5 2 -0.939 14.0067
11 H 1 _NW5 H9 2 0.398 1.0080
12 H 1 _NW5 H10 2 0.398 1.0080
13 NR 1 _NW5 N1 2 -0.841 14.0067
14 H 1 _NW5 H7 2 0.347 1.0080
15 C 1 _NW5 C1 2 0.040 12.0110
16 C 1 _NW5 C2 2 0.040 12.0110
17 C 1 _NW5 C3 2 -0.151 12.0110
18 C 1 _NW5 C5 2 0.150 12.0110
19 C 1 _NW5 C13 2 0.149 12.0110
20 HC 1 _NW5 H14 2 0.099 1.0080
21 NR 1 _NW5 N3 2 -0.567 14.0067
22 NR 1 _NW5 N4 2 0.436 14.0067 ; 0.000
23 C 1 _NW5 C10 3 -0.154 12.0110
24 HC 1 _NW5 H6 3 0.154 1.0080 ; 0.000
25 C 1 _NW5 C6 4 -0.154 12.0110
26 HC 1 _NW5 H3 4 0.154 1.0080 ; 0.000
27 C 1 _NW5 C4 5 -0.154 12.0110
28 HC 1 _NW5 H2 5 0.154 1.0080 ; 0.000
29 C 1 _NW5 C9 6 -0.152 12.0110
30 HC 1 _NW5 H5 6 0.152 1.0080 ; 0.000
31 C 1 _NW5 C7 7 -0.154 12.0110
32 HC 1 _NW5 H4 7 0.154 1.0080 ; 0.000
33 C 1 _NW5 C12 8 -0.200 12.0110
34 HC 1 _NW5 H15 8 0.200 1.0080 ; 0.000
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 22 2 0.1470 8.7100e+06
2 3 2 0.1090 1.2300e+07
2 4 2 0.1390 8.6600e+06
2 18 2 0.1435 6.1000e+06
4 5 2 0.1520 5.4300e+06
4 23 2 0.1435 6.1000e+06
5 6 2 0.1230 1.6600e+07
5 7 2 0.1380 1.1000e+07
7 8 2 0.1000 1.8700e+07
7 9 2 0.1400 8.5400e+06
9 10 2 0.1400 8.5400e+06
9 13 2 0.1320 1.2000e+07
10 11 2 0.1000 1.8700e+07
10 12 2 0.1000 1.8700e+07
13 14 2 0.1000 1.8700e+07
15 16 2 0.1435 6.1000e+06
15 17 2 0.1480 5.7300e+06
15 27 2 0.1390 8.6600e+06
16 18 2 0.1435 6.1000e+06
16 25 2 0.1435 6.1000e+06
17 19 2 0.1390 8.6600e+06
17 33 2 0.1390 8.6600e+06
18 31 2 0.1435 6.1000e+06
19 20 2 0.1090 1.2300e+07
19 21 2 0.1330 1.0600e+07
21 22 2 0.1360 4.7700e+06
22 33 2 0.1350 1.0300e+07
23 24 2 0.1090 1.2300e+07
23 25 2 0.1390 1.0800e+07
25 26 2 0.1090 1.2300e+07
27 28 2 0.1090 1.2300e+07
27 29 2 0.1435 6.1000e+06
29 30 2 0.1090 1.2300e+07
29 31 2 0.1390 1.0800e+07
31 32 2 0.1090 1.2300e+07
33 34 2 0.1090 1.2300e+07
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
2 6 1
2 7 1
4 8 1
4 9 1
5 10 1
5 13 1
6 8 1
6 9 1
6 23 1
7 11 1
7 12 1
7 14 1
7 23 1
8 10 1
8 13 1
10 14 1
11 13 1
12 13 1
16 19 1
16 33 1
19 27 1
27 33 1
[ angles ]
; ai aj ak funct angle fc
3 2 4 2 120.00 390.00
3 2 18 2 120.00 390.00
4 2 18 2 120.00 560.00
2 4 5 2 120.00 560.00
2 4 23 2 120.00 560.00
5 4 23 2 125.00 750.00
4 5 6 2 121.00 685.00
4 5 7 2 115.00 610.00
6 5 7 2 124.00 730.00
5 7 8 2 116.00 465.00
5 7 9 2 125.00 750.00
8 7 9 2 115.00 460.00
7 9 10 2 110.00 1280.00
7 9 13 2 120.00 560.00
10 9 13 2 125.00 750.00
9 10 11 2 116.00 465.00
9 10 12 2 115.00 460.00
11 10 12 2 109.50 285.00
9 13 14 2 109.50 285.00
16 15 17 2 120.00 560.00
16 15 27 2 120.00 560.00
17 15 27 2 120.00 560.00
15 16 18 2 120.00 560.00
15 16 25 2 125.00 750.00
18 16 25 2 120.00 560.00
15 17 19 2 132.00 760.00
15 17 33 2 126.00 640.00
19 17 33 2 105.00 1320.00
2 18 16 2 120.00 560.00
2 18 31 2 120.00 560.00
16 18 31 2 120.00 560.00
17 19 20 2 126.00 575.00
17 19 21 2 111.00 530.00
20 19 21 2 120.00 505.00
19 21 22 2 106.00 1690.00
1 22 21 2 119.00 1210.00
1 22 33 2 125.00 750.00
21 22 33 2 112.00 1400.00
4 23 24 2 120.00 390.00
4 23 25 2 120.00 560.00
24 23 25 2 120.00 390.00
16 25 23 2 120.00 560.00
16 25 26 2 120.00 390.00
23 25 26 2 120.00 390.00
15 27 28 2 120.00 390.00
15 27 29 2 120.00 560.00
28 27 29 2 120.00 390.00
27 29 30 2 120.00 390.00
27 29 31 2 120.00 560.00
30 29 31 2 120.00 390.00
18 31 29 2 120.00 560.00
18 31 32 2 120.00 390.00
29 31 32 2 120.00 390.00
17 33 22 2 108.00 465.00
17 33 34 2 131.00 927.00
22 33 34 2 121.40 690.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
15 27 29 31 2 0.00 167.36
27 29 31 18 2 0.00 167.36
29 31 18 16 2 0.00 167.36
31 18 16 15 2 0.00 167.36
18 16 15 27 2 0.00 167.36
16 15 27 29 2 0.00 167.36
17 19 21 22 2 0.00 167.36
19 21 22 33 2 0.00 167.36
21 22 33 17 2 0.00 167.36
22 33 17 19 2 0.00 167.36
33 17 19 21 2 0.00 167.36
16 25 23 4 2 0.00 167.36
25 23 4 2 2 0.00 167.36
23 4 2 18 2 0.00 167.36
4 2 18 16 2 0.00 167.36
2 18 16 25 2 0.00 167.36
18 16 25 23 2 0.00 167.36
15 16 17 27 2 0.00 167.36
16 15 18 25 2 0.00 167.36
17 15 19 33 2 0.00 167.36
27 15 28 29 2 0.00 167.36
18 2 16 31 2 0.00 167.36
25 16 23 26 2 0.00 167.36
31 18 29 32 2 0.00 167.36
2 3 4 18 2 0.00 167.36
29 27 30 31 2 0.00 167.36
23 4 24 25 2 0.00 167.36
4 2 5 23 2 0.00 167.36
33 17 22 34 2 0.00 167.36
19 17 20 21 2 0.00 167.36
5 4 6 7 2 0.00 167.36
9 7 10 13 2 0.00 167.36
7 5 8 9 2 0.00 167.36
22 1 21 33 2 0.00 167.36
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
2 4 5 7 1 180.00 33.50 2
4 5 7 9 1 180.00 33.50 2
5 7 9 13 1 180.00 33.50 2
13 9 10 11 1 180.00 33.50 2
7 9 13 14 1 180.00 33.50 2
16 15 17 33 1 180.00 1.53 2
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions
1 17
1 19
1 34
2 15
2 24
2 25
2 29
2 32
3 5
3 16
3 23
3 31
4 16
4 26
4 31
5 18
5 24
5 25
15 20
15 21
15 22
15 23
15 26
15 30
15 31
15 34
16 24
16 28
16 29
16 32
17 18
17 25
17 28
17 29
18 23
18 26
18 27
18 30
19 34
20 22
20 33
21 34
24 26
25 27
25 31
27 32
28 30
28 31
30 32
--
With Regards
Monoj Mon Kalita
Institute of Biophotonics<http://www.ym.edu.tw/biophotonics/eng_version/home.htm>
Fischer's Lab <http://www.ym.edu.tw/%7Ewfischer/group_mon.htm>
National Yang-Ming University<http://nymu-e.web.ym.edu.tw/front/bin/home.phtml>
Taipei, Taiwan
mon.123chem at gmail.com
More information about the gromacs.org_gmx-users
mailing list