[gmx-users] Unknown bond_atomtype CG2O2
Steven Neumann
s.neumann08 at gmail.com
Thu Feb 7 11:16:34 CET 2013
Dear Gmx users,
I know this subject has been discussed but I still did not find the answer.
I have topology of my molecule:
ligand.rtp
[ GUY ] ; CGenFF output = RESI aR_citri 0.000 ! param penalty= 46.200
; charge penalty= 28.481
[ atoms ]
C1 CG301 0.125 0
C2 CG321 -0.197 1
C3 CG321 -0.197 2
C4 CG2O2 0.848 3
O5 OG311 -0.642 4
C6 CG2O2 0.768 5
C7 CG2O2 0.768 6
O8 OG311 -0.642 7
O9 OG2D1 -0.538 8
O10 OG311 -0.632 9
O11 OG2D1 -0.549 10
O12 OG311 -0.632 11
O13 OG2D1 -0.549 12
H14 HGA2 0.090 13
H15 HGA2 0.090 14
H16 HGA2 0.090 15
H17 HGA2 0.090 16
H18 HGP1 0.419 17
H19 HGP1 0.430 18
H20 HGP1 0.430 19
H21 HGP1 0.430 20
[ bonds ]
H19 O8
O8 C4
C4 O9
C4 C1
H17 C3
H14 C2
H20 O10
O11 C6
O10 C6
C6 C2
C3 C7
C3 C1
C3 H16
O12 H21
O12 C7
C2 C1
C2 H15
C7 O13
C1 O5
O5 H18
[ impropers ]
C4 C1 O9 O8
C6 C2 O11 O10
C7 C3 O13 O12
Which is already in my working directory ff.
I added to ffbonded.itp
[ bondtypes ]
; i j func b0 kb
CG2O2 CG301 1 0.1522 167360
CG2O2 CG321 1 0.1522 167360
CG2O2 OG2D1 1 0.122 627600
CG2O2 OG311 1 0.14 192464
CG301 CG321 1 0.1538 186188
CG301 OG311 1 0.142 358150.4
CG321 HGA2 1 0.1111 258571.2
OG311 HGP1 1 0.096 456056
[ angletypes ]
; i j k func th0 cth ub0 cub
CG301 CG2O2 OG2D1 5 125.00 585.76
0.2442 16736
CG301 CG2O2 OG311 5 110.50 460.24 0
0
CG321 CG2O2 OG2D1 5 125.00 585.76
0.2442 16736
CG321 CG2O2 OG311 5 110.50 460.24 0
0
OG2D1 CG2O2 OG311 5 123.00 418.4
0.2262 175728
CG2O2 CG301 CG321 5 108.00 435.136 0
0
CG2O2 CG301 OG311 5 122.50 937.216 0
0
CG321 CG301 CG321 5 113.50 488.2728
0.2561 9338.688
CG321 CG301 OG311 5 110.10 633.4576 0
0
CG2O2 CG321 CG301 5 108.00 435.136 0
0
CG2O2 CG321 HGA2 5 109.50 276.144
0.2163 25104
CG301 CG321 HGA2 5 110.10 221.752
0.2179 18853.104
HGA2 CG321 HGA2 5 109.00 297.064
0.1802 4518.72
CG2O2 OG311 HGP1 5 115.00 460.24 0
0
CG301 OG311 HGP1 5 106.00 418.4 0
0
[ dihedraltypes ]
; i j k l func phi0 cp mult
OG2D1 CG2O2 CG301 CG321 9 180.00
0.2092 6
OG2D1 CG2O2 CG301 OG311 9 0.00 0
2
OG311 CG2O2 CG301 CG321 9 180.00
0.2092 6
OG311 CG2O2 CG301 OG311 9 180.00 0
6
OG2D1 CG2O2 CG321 CG301 9 180.00 0
6
OG2D1 CG2O2 CG321 HGA2 9 180.00 0
6
OG311 CG2O2 CG321 CG301 9 180.00 0
6
OG311 CG2O2 CG321 HGA2 9 180.00 0
6
CG301 CG2O2 OG311 HGP1 9 180.00
8.5772 2
CG321 CG2O2 OG311 HGP1 9 180.00
8.5772 2
OG2D1 CG2O2 OG311 HGP1 9 180.00
8.5772 2
CG2O2 CG301 CG321 CG2O2 9 0.00
0.8368 3
CG2O2 CG301 CG321 HGA2 9 0.00
0.8368 3
CG321 CG301 CG321 CG2O2 9 180.00
0.87864 1
CG321 CG301 CG321 CG2O2 9 0.00
1.63176 2
CG321 CG301 CG321 CG2O2 9 180.00
1.4644 3
CG321 CG301 CG321 CG2O2 9 0.00
0.46024 4
CG321 CG301 CG321 CG2O2 9 180.00
0.37656 6
CG321 CG301 CG321 HGA2 9 0.00
0.81588 3
OG311 CG301 CG321 CG2O2 9 0.00
0.8368 3
OG311 CG301 CG321 HGA2 9 0.00
0.66944 3
CG2O2 CG301 OG311 HGP1 9 0.00
0.92048 1
CG2O2 CG301 OG311 HGP1 9 180.00
0.96232 2
CG2O2 CG301 OG311 HGP1 9 0.00
1.75728 3
CG321 CG301 OG311 HGP1 9 0.00
4.72792 1
CG321 CG301 OG311 HGP1 9 0.00
0.58576 2
CG321 CG301 OG311 HGP1 9 0.00
1.00416 3
[ dihedraltypes ]
; i j k l func q0 cp
CG2O2 CG301 OG2D1 OG311 2 0.00 543.92
CG2O2 CG321 OG2D1 OG311 2 0.00 543.92
and all the atomtypes are in my atomtypes.atp:
CG2O2 12.01100
CG301 12.01100
...
I run pdb2gmx producing the topology.
But when I try grompp:
Fatal error:
Unknown bond_atomtype CG2O2
Can you hel please?
Steven
More information about the gromacs.org_gmx-users
mailing list