[gmx-users] Citrate topology in Charmm36 FF
Pandya, Akash
akash.pandya.15 at ucl.ac.uk
Mon Jun 17 15:15:37 CEST 2019
Hi all,
I'm simulating Citrate in water using the Charmm36 FF. I get this error in my topology. I have used the same topology for charmm27 ff and had no problems.
ERROR 1 [file CITMolecule.itp, line 63]:
No default Bond types
ERROR 2 [file CITMolecule.itp, line 64]:
No default Bond types
ERROR 3 [file CITMolecule.itp, line 71]:
No default Bond types
ERROR 4 [file CITMolecule.itp, line 72]:
No default Bond types
ERROR 5 [file CITMolecule.itp, line 81]:
No default U-B types
ERROR 6 [file CITMolecule.itp, line 82]:
No default U-B types
ERROR 7 [file CITMolecule.itp, line 84]:
No default U-B types
ERROR 8 [file CITMolecule.itp, line 97]:
No default U-B types
ERROR 9 [file CITMolecule.itp, line 98]:
No default U-B types
ERROR 10 [file CITMolecule.itp, line 100]:
No default U-B types
My topology file is pasted here with the relevant parts:
[ bondtypes ]
CC OC 1 0.126 439320.0
OH1 H 1 0.096 456056.0
CT CC 1 0.152 167360.0
CT2 CT 1 0.150 186188.0
CT OH1 1 0.142 358150.4
[ angletypes ]
OC CC OC 5 124.00 836.80 0.2225 58576.000
OC CC CT2 5 118.00 334.72 0.2388 41840.000
CT CC OC 5 118.00 334.72 0.2388 41840.000
CT2 CT CC 5 108.00 435.14 0.0000 0.000
CT2 CT CT2 5 113.60 488.27 0.2561 9338.688
HA CT2 CT 5 110.10 279.74 0.2179 18853.104
CC CT2 CT 5 108.00 435.14 0.0000 0.000
CT2 CT OH1 5 110.10 633.46 0.0000 0.000
OH1 CT CC 5 110.10 633.46 0.0000 0.000
CT OH1 H 5 106.00 481.16 0.0000 0.000
[ dihedraltypes ]
HA CT2 CC OC 9 180.00 0.2092 6
CT CT2 CC OC 9 180.00 0.2092 6
CT2 CT CT2 CC 9 0.00 4.0000 3
OH1 CT CT2 CC 9 0.00 0.8368 3
OH1 CT CT2 HA 9 0.00 0.8368 3
CC CT CT2 CC 9 0.00 0.8368 3
CC CT CT2 HA 9 0.00 0.8368 3
CT2 CT CT2 HA 9 0.00 0.8368 3
OH1 CT CC OC 9 0.00 1.2000 2
CT2 CT CC OC 9 180.00 0.2092 6
CC CT OH1 H 9 0.00 0.2092 1
CT2 CT OH1 H 9 0.00 0.5858 3
CC CT2 OC OC 2 0.00 803.328
CC CT OC OC 2 0.00 803.328
[ moleculetype ]
CIT 3
[ atoms ]
1 CC 1 CIT C 1 0.620 12.011
2 CT2 1 CIT C 2 -0.180 12.011
3 CT 1 CIT C 3 -0.070 12.011
4 CC 1 CIT C 4 0.620 12.011
5 CT2 1 CIT C 5 -0.180 12.011
6 CC 1 CIT C 6 0.620 12.011
7 OC 1 CIT O 7 -0.760 15.999
8 OC 1 CIT O 8 -0.760 15.999
9 OC 1 CIT O 9 -0.760 15.999
10 OC 1 CIT O 10 -0.760 15.999
11 OC 1 CIT O 11 -0.760 15.999
12 OC 1 CIT O 12 -0.760 15.999
13 OH1 1 CIT O 13 -0.540 15.999
14 HA 1 CIT H 14 0.090 1.008
15 HA 1 CIT H 15 0.090 1.008
16 HA 1 CIT H 16 0.090 1.008
17 HA 1 CIT H 17 0.090 1.008
18 H 1 CIT H 18 0.310 1.008
[ bonds ]
1 8 1
1 7 1
1 2 1
2 15 1
2 14 1
2 3 1
3 13 1
3 5 1
3 4 1
4 10 1
4 9 1
5 17 1
5 16 1
5 6 1
6 12 1
6 11 1
13 18 1
[ angles ]
8 1 7 5
8 1 2 5
7 1 2 5
1 2 15 5
15 2 14 5
15 2 3 5
1 2 14 5
14 2 3 5
1 2 3 5
2 3 13 5
13 3 5 5
13 3 4 5
2 3 5 5
5 3 4 5
2 3 4 5
3 4 10 5
10 4 9 5
3 4 9 5
3 5 17 5
17 5 16 5
17 5 6 5
3 5 16 5
16 5 6 5
3 5 6 5
5 6 12 5
12 6 11 5
5 6 11 5
3 13 18 5
[ exclusions ]
18 9 10
[ pairs ]
10 18 2 0.3 -0.760 0.310 0.17145 0.310857
9 18 2 0.3 -0.760 0.310 0.17145 0.310857
[ dihedrals ]
8 1 2 15 9
7 1 2 15 9
8 1 2 14 9
7 1 2 14 9
8 1 2 3 9
7 1 2 3 9
1 2 3 13 9
15 2 3 13 9
14 2 3 13 9
1 2 3 5 9
15 2 3 5 9
14 2 3 5 9
1 2 3 4 9
15 2 3 4 9
14 2 3 4 9
2 3 13 18 9
5 3 13 18 9
4 3 13 18 9
2 3 5 17 9
13 3 5 17 9
4 3 5 17 9
2 3 5 16 9
13 3 5 16 9
4 3 5 16 9
2 3 5 6 9
13 3 5 6 9
4 3 5 6 9
2 3 4 10 9
13 3 4 10 9
5 3 4 10 9
2 3 4 9 9
13 3 4 9 9
5 3 4 9 9
3 5 6 12 9
17 5 6 12 9
16 5 6 12 9
3 5 6 11 9
17 5 6 11 9
16 5 6 11 9
[ dihedrals ]
1 2 7 8 2
4 3 9 10 2
6 5 11 12 2
#ifdef POSRES_CITMolecule
[ 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
11 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
#endif
Please can you advise me on what to do. I have referred to the manual but I am not getting any luck.
Akash
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