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

--
========================================

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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