[gmx-users] RE: No default Proper Dih. types

[Justin Lemkul]

On 1/16/13 10:58 AM, escajarro wrote:
> Hello all,
>
> I have the same problem, but I think the dihedral is properly defined.
>
> I am running a polymer with the G53A6 force field. First I use pdb2gmx to
> generate a conf and a top file. When I run grompp, I have the error(s):
>
> ERROR 1 [file topol.top, line 1507]:
>    No default Proper Dih. types
>
> Then I go to the topol.top file, line 1507, which contains, inside the [
> dihedrals ] directive:
>
>      1     2    10    11     1
>
> It is clear that it does not have a torsion type defined for this atoms. I
> look at the beginning of the same top file, to know of what type are atoms
> 1, 2, 10, and 11, and in what residue they are:
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
>       1        CH3      1    MEA     CB      1          0     15.035   ; qtot
> 0
>       2        CH1      2    NIP    CA1      2          0     13.019   ; qtot
> 0
>       3          C      2    NIP      C      3       0.45     12.011   ; qtot
> 0.45
>       4          O      2    NIP      O      3      -0.45    15.9994   ; qtot
> 0
>       5          N      2    NIP      N      4      -0.31    14.0067   ; qtot
> -0.31
>       6          H      2    NIP      H      4       0.31      1.008   ; qtot
> 0
>       7        CH1      2    NIP    CA2      5          0     13.019   ; qtot
> 0
>       8        CH3      2    NIP    CB1      5          0     15.035   ; qtot
> 0
>       9        CH3      2    NIP    CB2      5          0     15.035   ; qtot
> 0
>      10        CH2      3    MEM     CB      6          0     14.027   ; qtot
> 0
>      11        CH1      4    NIP    CA1      7          0     13.019   ; qtot
> 0
> ...etc
>
> Now I look to my aminoacids.rtp file. There I have the residues defined:
>
> [ MEA ]
>   [ atoms ]
>     CB     CH3          0.000    1
>   [ bonds ]
>
> [ MEM ]
>   [ atoms ]
>     CB     CH2          0.000    1
>   [ bonds ]
>     CB   -CA1  gb_27
>   [ angles ]
>     CB  -CA1  -CB  ga_15
>
> [ MEE ]
>   [ atoms ]
>     CB     CH3          0.000    1
>   [ bonds ]
>     CB   -CA1  gb_27
>   [ angles ]
>    -CB   -CA1   CB   ga_15
>
> [ NIP ]
>   [ atoms ]
>     CA1    CH1         0.000     1
>     C      C           0.450     2
>     O      O          -0.450     2
>     N      N          -0.310     3
>     H      H           0.310     3
>     CA2    CH1         0.000     4
>     CB1    CH3         0.000     4
>     CB2    CH3         0.000     4
>   [ bonds ]
>     CA1  C     gb_27
>     C    O     gb_5
>     C    N     gb_11
>     N    H     gb_2
>     N    CA2   gb_21
>     CA2  CB1   gb_27
>     CA2  CB2   gb_27
>     CA1  -CB   gb_27
> [ angles ]
>     -CB  CA1  +CB   ga_15
>     -CB  CA1   C    ga_13
>      C   CA1  +CB   ga_13
>      CA1  C    O    ga_30
>      CA1  C    N    ga_19
>      O    C    N    ga_33
>      C    N    H    ga_32
>      C    N    CA2  ga_31
>      H    N    CA2  ga_18
>      N    CA2  CB1  ga_13
>      N    CA2  CB2  ga_13
>      CB1  CA2  CB2  ga_15
>      CA1 +CB  +CA1  ga_15
>   [ dihedrals ]
>     -CB   CA1 +CB  +CA1  gd_34
>     -CB   CA1  C    N    gd_40
>      CA1  C    N    CA2  gd_14
>      C    N    CA2  CB1  gd_39
>      CA1 +CB  +CA1 +C    gd_34
>   [ impropers ]
>      CA1 -CB  +CB   C    gi_2
>      C    CA1  N    O    gi_1
>      N    C    CA2  H    gi_1
>      CA2  N    CB1  CB2  gi_2
>
> As I understand it, the torsion grompp is complaining about is the first
> torsion defined in the NIP residue. I have tried, just in case, to write
> that torsion in different ways, at a different order, in the residue MEM,
> changing atom names to the name they have in atomtypes.atp... but without
> success.
>
> Any idea what happens?
>

Atom names and .rtp files are largely irrelevant here.  You have a torsion 
specified with atom types CH3-CH1-CH2-CH1.  If there are no parameters in 
ffbonded.itp for that interaction, grompp is going to give you that error message.

-Justin

-- 
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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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