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

[escajarro]

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?

Kind regards



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