[gmx-users] Vacuum: still struggling with lig.itp

[Pedro Alexandre Lapido Loureiro]

Hi!

I think you forgot to write the "function" column in the [bonds], [angles],
[dihedrals] and [impropers] items. Its value is "2" (except for [dihedrals] - in
that case it`s "1"), but check the manual.

Regards.



 
> [ moleculetype ]
>  ;name nrexcl
> DRG      3
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB     massB
>     1       CH3     285   DRG     CAO      1       0.000    15.035
>     2         C     285   DRG     CAM      1       0.380    12.011
>     3         O     285   DRG     OAN      1      -0.380   15.9994
>     4         N     285   DRG     NAL      2      -0.280   14.0067
>     5         H     285   DRG     HAB      2       0.280     1.008
>     6       CH2     285   DRG     CAK      3       0.000    14.027
>     7       CH2     285   DRG     CAJ      3       0.000    14.027
>     8         C     285   DRG     CAA      4      -0.140    12.011
>     9         C     285   DRG     CAC      4       0.000    12.011
>    10       CR1     285   DRG     CAF      5       0.000    13.019
>    11         C     285   DRG     CAH      5       0.100    12.011
>    12        OA     285   DRG     OAP      6      -0.100   15.9994
>    13       CH3     285   DRG     CAQ      6       0.000    15.035
>    14       CR1     285   DRG     CAI      7       0.000    13.019
>    15       CR1     285   DRG     CAG      7       0.000    13.019
>    16         C     285   DRG     CAE      8       0.000    12.011
>    17        NR     285   DRG     NAD      8      -0.050   14.0067
>    18         H     285   DRG     HAA      8       0.190     1.008
>    19       CR1     285   DRG     CAB      8       0.000    13.019
> [ bonds ]
>   1   2    gb_26
>   2   3    gb_4
>   2   4    gb_9
>   4   5    gb_2
>   4   6    gb_20
>   6   7    gb_26
>   7   8    gb_14
>   8   19    gb_9
>   8   9    gb_9
>   19   17    gb_9
>   17   18    gb_2
>   17   16    gb_9
>   16   9    gb_15
>   9   10    gb_15
>   10   11    gb_15
>   11   14    gb_15
>   14   15    gb_15
>   15   16    gb_15
>   11   12    gb_12
>   12   13    gb_17
>  [ angles ]
> ;   ai    aj    ak  gromos type
>   1   2   3    ga_29
>   1   2   4    ga_18
>   3   2   4    ga_32
>   2   4   5    ga_31
>   2   4   6    ga_30
>   5   4   6    ga_17
>   4   6   7    ga_12
>   6   7   8    ga_14
>   7   8   19    ga_36
>   8   19   17    ga_6
>   19   17   18    ga_35
>   19   17   16    ga_6
>   19   8   9    ga_6
>   8   9   16    ga_6
>   9   16   17    ga_6
>   17   16   15    ga_38
>   8   9   10    ga_38
>   16   9   10    ga_26
>   9   10   11    ga_26
>   10   11   14    ga_26
>   11   14   15    ga_26
>   14   15   16    ga_26
>   15   16   9    ga_26
>   10   11   12    ga_18
>   11   12   13    ga_11
>   14   11   12    ga_18
>  [ impropers ]
> ;   ai    aj    ak    al  gromos type
>   2   1   4   3    gi_1
>   4   2   5   6    gi_1
>   8   19   9   7    gi_1
>   9   8   16   10    gi_1
>   11   14   12   10    gi_1
>   16   9   15   17    gi_1
>   17   16   18   19    gi_1
>   8   9   16   17    gi_1
>   9   16   17   19    gi_1
>   16   17   19   8    gi_1
>   17   19   8   9    gi_1
>   19   8   9   16    gi_1
>   9   10   11   14    gi_1
>   10   11   14   15    gi_1
>   11   14   15   16    gi_1
>   14   15   16   9    gi_1
>   15   16   9   10    gi_1
>   16   9   10   11    gi_1
> 
>  [ dihedrals ]
> ;   ai    aj    ak    al  gromos type
>   1   2   4   6    gd_4
>   7   6   4   2    gd_19
>   8   7   6   4    gd_17
>   19   8   7   6    gd_20
>   10   11   12   13    gd_2
> 


--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil