[gmx-users] Fatal error: Atom O in residue COC 1 not found in rtp entry with 22 atoms
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Wed Nov 24 09:09:26 CET 2004
On Tuesday 23 November 2004 20:23, Yunfeng Hu wrote:
> 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
Have you used the right force field with pdb2gmx ?
>
>
> 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
>
Greetings,
Florian
--
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Florian Haberl Universitaet Erlangen/
Computer-Chemie-Centrum Nuernberg
Naegelsbachstr. 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
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