[gmx-users] Fatal error: Atom O in residue COC 1 not found in rtp entry with 22 atoms
Yunfeng Hu
yunfeng at scripps.edu
Tue Nov 23 20:23:18 CET 2004
Hi, I edited ffG43a1.rtp and ffG43a1.hdb to incorporate my new ligand.
However I still get the following error when using pdb2gmx -ignh -f
cocaine.pdb -o cocaine.gro -p cocaine.top
Back Off! I just backed up cocaine.top to ./#cocaine.top.3#
Processing chain 1 'X' (22 atoms, 1 residues)
Opening library file /usr/local/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 1 acceptors
There are 0 hydrogen bonds
Fatal error: Atom O in residue COC 1 not found in rtp entry with 22
atoms
while sorting atoms
The pdb file looks like this:
ATOM 3374 O7 COC X 1 40.826 23.990 -6.188
ATOM 3375 C6 COC X 1 41.855 23.346 -6.031
ATOM 3376 O5 COC X 1 43.100 23.859 -6.283
ATOM 3377 C1 COC X 1 43.125 25.101 -7.037
ATOM 3381 C8 COC X 1 41.854 21.926 -5.478
ATOM 3383 C10 COC X 1 40.782 21.024 -6.183
ATOM 3385 N12 COC X 1 39.443 21.611 -5.859
ATOM 3386 C14 COC X 1 38.377 21.175 -6.848
ATOM 3390 C24 COC X 1 39.201 21.271 -4.432
ATOM 3392 C18 COC X 1 40.709 19.663 -5.469
ATOM 3395 C21 COC X 1 39.653 19.793 -4.347
ATOM 3398 C29 COC X 1 41.619 21.896 -3.941
ATOM 3400 C26 COC X 1 40.147 22.203 -3.603
ATOM 3403 O1 COC X 1 42.405 22.932 -3.318
ATOM 3404 C2 COC X 1 43.680 22.607 -2.938
ATOM 3405 O3 COC X 1 44.285 21.597 -3.331
ATOM 3406 C4 COC X 1 44.280 23.567 -1.979
ATOM 3407 C5 COC X 1 45.663 23.521 -1.718
ATOM 3409 C7 COC X 1 46.209 24.423 -0.791
ATOM 3411 C9 COC X 1 45.370 25.347 -0.194
ATOM 3413 C11 COC X 1 44.005 25.423 -0.455
ATOM 3415 C13 COC X 1 43.443 24.514 -1.364
Here are the added hdb and rtp portions.
COC 14
1 1 C5 C4 C7
1 1 C7 C5 C9
1 1 C9 C7 C11
1 1 C11 C9 C13
1 1 C13 C4 C11
1 5 C8 C10 C29
1 5 C10 C8 C18
1 5 C24 C21 C26
1 5 C29 C8 C26
2 6 C18 C10 C21
2 6 C21 C18 C24
2 6 C26 C24 C29
3 4 C1 O5 C6
3 4 C14 N12 C10
[ COC ]
[ atoms ]
C1 CH3 0.078 1
O5 OA -0.110 1
C6 C 0.531 1
O7 O -0.499 1
C8 CH1 0.127 2
C10 CH1 0.127 2
N12 NL -0.300 2
C14 CH3 0.046 2
C18 CH2 0.000 3
C21 CH2 0.000 3
C24 CH1 0.000 4
C26 CH2 0.100 5
C29 CH1 0.258 5
O1 OA -0.141 5
C2 C 0.418 5
O3 O -0.635 5
C4 C 0.015 6
C5 CR1 -0.007 6
C7 CR1 -0.008 6
C9 CR1 0.000 7
C11 CR1 0.000 7
C11 CR1 0.000 7
C13 CR1 0.000 7
[ bonds ]
C1 O5 gb_17
O5 C6 gb_12
C6 O7 gb_4
C6 C8 gb_26
C8 C10 gb_26
C8 C29 gb_26
C10 N12 gb_20
C10 C18 gb_26
N12 C14 gb_20
N12 C24 gb_20
C18 C21 gb_26
C21 C24 gb_26
C24 C26 gb_26
C26 C29 gb_26
C29 O1 gb_17
O1 C2 gb_12
C2 O3 gb_4
C2 C4 gb_26
C4 C5 gb_15
C4 C13 gb_15
C5 C7 gb_15
C7 C9 gb_15
C9 C11 gb_15
C11 C13 gb_15
[ angles ]
; ai aj ak gromos type
C1 O5 C6 ga_11
O5 C6 O7 ga_29
O5 C6 C8 ga_29
O7 C6 C8 ga_29
C6 C8 C10 ga_7
C6 C8 C29 ga_7
C10 C8 C29 ga_14
C8 C10 N12 ga_12
C8 C10 C18 ga_14
N12 C10 C18 ga_5
C10 N12 C14 ga_9
C10 N12 C24 ga_9
C14 N12 C24 ga_9
C10 C18 C21 ga_5
C18 C21 C24 ga_5
N12 C24 C21 ga_5
N12 C24 C26 ga_12
C21 C24 C26 ga_7
C24 C26 C29 ga_7
C8 C29 C26 ga_7
C8 C29 O1 ga_12
C26 C29 O1 ga_12
C29 O1 C2 ga_11
O1 C2 O3 ga_29
O1 C2 C4 ga_29
O3 C2 C4 ga_29
C2 C4 C5 ga_26
C2 C4 C13 ga_26
C5 C4 C13 ga_26
C4 C5 C7 ga_26
C5 C7 C9 ga_26
C7 C9 C11 ga_26
C9 C11 C13 ga_26
C4 C13 C11 ga_26
[ dihedrals ]
C6 O5 C8 O7 gi_1
C2 O1 C4 O3 gi_1
C4 C13 C5 C2 gi_1
C8 C6 C10 C29 gi_2
C10 C8 N12 C18 gi_2
N12 C10 C24 C14 gi_2
C24 N12 C26 C21 gi_2
C29 C8 C26 O1 gi_2
C4 C5 C7 C9 gi_1
C5 C7 C9 C11 gi_1
C7 C9 C11 C13 gi_1
C9 C11 C13 C4 gi_1
C11 C13 C4 C5 gi_1
C13 C4 C5 C7 gi_1
C1 O5 C6 C8 gd_3
C29 C8 C6 O5 gi_1
C18 C10 C8 C6 gi_1
C6 C8 C29 O1 gi_1
C8 C10 N12 C24 gi_1
C21 C18 C10 C8 gi_1
C26 C24 N12 C10 gi_1
C24 C21 C18 C10 gi_1
C18 C21 C24 C26 gi_1
C29 C26 C24 N12 gi_1
O1 C29 C26 C24 gi_1
C8 C29 O1 C2 gi_1
C29 O1 C2 C4 gd_3
C13 C4 C2 O1 gd_1
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