[gmx-users] Unknown bond_atomtype CG2O2
Justin Lemkul
jalemkul at vt.edu
Thu Feb 7 13:05:07 CET 2013
On 2/7/13 5:16 AM, Steven Neumann wrote:
> 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
>
New atom types must also be added to atomtypes.atp and ffnonbonded.itp. The
error means the atom type is found in a bonded interaction, but it is an unknown
type in the context of the rest of the force field.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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