[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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