[gmx-users] OPLS force field does not recognize Atom type

Morteza Khabiri khabiri at greentech.cz
Tue Sep 9 22:03:36 CEST 2008


Dear
I want to make the solution which is not working with unified atom force
fields. Then I decided to make the itp file by my own.
I made the all atom type ....itp file for opls AA. I found all of the opls
feature in gromacs top directory and according to the top directory files
I made the new itp file. Unfortunately, after running the grompp i faced
with the following error:
   Fatal error:
                   Atomtype 'HC' not found!
but it is defined in the opls.

My itp file structure is like follow:
;
[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        HC     1  DRG     HAD     1    0.02734   1.0080
     2        CT     1  DRG     CAL     1    0.10638  12.0110
     3        HC     1  DRG     HAE     1    0.02734   1.0080
     4        OS     1  DRG     OAI     1   -0.36111  15.9994
     5        CT     1  DRG     CAK     1    0.10638  12.0110
     6        HC     1  DRG     HAB     2    0.02734   1.0080
     7        HC     1  DRG     HAG     2    0.02734   1.0080
     8        CY     1  DRG     CAM     2    0.00235  12.0110
     9        HC     1  DRG     HAF     3    0.00857   1.0080
    10        HC     1  DRG     HAH     3    0.00857   1.0080
    11        CY     1  DRG     CAJ     3    0.00235  12.0110
    12        HC     1  DRG     HAC     3    0.00857   1.0080
    13        HC     1  DRG     HAA     3    0.00857   1.0080

[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   1    0.109    284512.0    0.109    284512.0 ;   HAD  CAL
   2   3   1    0.109    284512.0    0.109    284512.0 ;   CAL  HAE
   2   4   1    0.141    267776.0    0.141    267776.0 ;   CAL  HAI
   2  11   1    0.152    217568.0    0.152    217568.0 ;   CAL  CAJ
   4   5   1    0.141    267776.0    0.141    267776.0 ;   OAI  CAK
   5   6   1    0.109    284512.0    0.109    284512.0 ;   CAK  HAB
   5   7   1    0.109    284512.0    0.109    284512.0 ;   CAK  HAG
   5   8   1    0.151    234304.0    0.151    234304.0 ;   CAK  CAM
   8   9   1    0.108    284512.0    0.108    284512.0 ;   CAM  HAF
   8  10   1    0.108    284512.0    0.108    284512.0 ;   CAM  HAH
   8  11   1    0.150    217568.0    0.150    217568.0 ;   CAM  CAJ
  11  12   1    0.108    284512.0    0.108    284512.0 ;   CAJ  HAC
  11  13   1    0.108    284512.0    0.108    284512.0 ;   CAJ  HAA

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   5   1                                           ;   HAD  CAK
   1   8   1                                           ;   HAD  CAM
   1  12   1                                           ;   HAD  HAC
   1  13   1                                           ;   HAD  HAA
   2   6   1                                           ;   CAL  HAB
   2   7   1                                           ;   CAL  HAG
   2   9   1                                           ;   CAL  HAF
   2  10   1                                           ;   CAL  HAH
   3   5   1                                           ;   HAE  CAK
   3   8   1                                           ;   HAE  CAM
   3  12   1                                           ;   HAE  HAC
  6   9   1                                           ;   HAB  HAF
   8  10   1                                           ;   HAB  HAH
   6  11   1                                           ;   HAB  CAJ
   7   9   1                                           ;   HAG  HAF
   7  10   1                                           ;   HAG  HAH
   7  11   1                                           ;   HAG  CAJ
   9  12   1                                           ;   HAF  HAC
   9  13   1                                           ;   HAF  HAA
  10  12   1                                           ;   HAH  HAC
  10  13   1                                           ;   HAH  HAA

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   1    107.8       276.1    107.8       276.1 ;   HAD  CAL  HAE
   1   2   4   1    109.5       292.8    109.5       292.8 ;   HAD  CAL  OAI
   1   2  11   1    110.7       313.8    109.5       397.5 ;   HAD  CAL  CAJ
   3   2   4   1    109.5       292.8    109.5       292.8 ;   HAE  CAL  OAI
   3   2  11   1    110.7       313.8    110.7       313.8 ;   HAE  CAL  CAJ
   4   2  11   1    109.5       292.8    109.5       292.8 ;   OAI  CAL  CAJ
   2   4   5   1    109.5       502.0    109.5       502.0 ;   CAL  OAI  CAK
   4   5   6   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  HAB
   4   5   7   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  HAG
   4   5   8   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  CAM
   6   5   7   1    107.8       276.1    107.8       276.1 ;   HAB  CAK  HAG
   6   5   8   1    110.7       313.8    110.7       313.8 ;   HAB  CAK  CAM
   7   5   8   1    110.7       313.8    110.7       313.8 ;   HAG  CAK  CAM
   5   8   9   1    114.3       292.8    114.3       292.8 ;   CAK  CAM  HAF
   5   8  10   1    114.3       292.8    114.3       292.8 ;   CAK  CAM  HAH
   5   8  11   1    117.2       313.8    117.2       313.8 ;   CAK  CAM  CAJ
   9   8  10   1    114.3       292.8    114.3       292.8 ;   HAF  CAM  HAH
   9   8  11   1    117.2       313.8    117.2       313.8 ;   HAF  CAM  CAJ
  10   8  11   1    117.2       313.8    117.2       313.8 ;   HAH  CAM  CAJ
   2  11   8   1    117.2       313.8    117.2       313.8 ;   CAL  CAJ  CAM
   2  11  12   1    114.3       292.8    114.3       292.8 ;   CAL  CAJ  HAC
   2  11  13   1    114.3       292.8    114.3       292.8 ;   CAL  CAJ  HAA
   8  11  12   1    117.2       313.8    117.2       313.8 ;   CAM  CAJ  HAC
   8  11  13   1    117.2       313.8    117.2       313.8 ;   CAM  CAJ  HAA
  12  11  13   1    114.3       292.8    114.3       292.8 ;   HAC  CAJ  HAA

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1   3   4   3     1.58  4.769       1.58  4.769   ; imp   CAL  HAD 
HAE  OAI
   5   4   6   7   3     1.58  4.769       1.58  4.769   ; imp   CAK  OAI 
HAB  HAG
   8   5  10   9   3     0.62  1.882       0.62  1.882   ; imp   CAM  CAK 
HAH  HAF
  11   2  12   8   3     0.62  1.882       0.62  1.882   ; imp   CAJ  CAL 
HAC  CAM
   1   2   4   5   3      1.5    4.7 3      1.5    4.7 3 ; dih   HAD  CAL 
OAI  CAK
  13  11   2   1   3      1.5    4.7 3      1.5    4.7 3 ; dih   HAA  CAJ 
CAL  HAD
   2   4   5   8   3      1.5    4.7 3      1.5    4.7 3 ; dih   CAL  OAI 
CAK  CAM
  11   8   5   4   3      1.5    4.7 3      1.5    4.7 3 ; dih   CAJ  CAM 
CAK  OAI
  13  11   8   5   3      0.6    1.8 3      0.6    1.8 3 ; dih   HAA  CAJ 
CAM  CAK


The top file is also set to OPLS forcefield.

I don't know what is wrong exactly. Thats very nice of you if you could
help me.

Thank you very much in advance

Morteza





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