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

[Martina Bertsch, PhD]

Hi, David and Anton.

Thanks for your replies.

Even before I received Anton's message, I manually edited the ligand itp 
file created by PRODRG to include the ffG43a1 parameters. To make 
assignment easier, I listed all the bonds, angles, etc. as combinations 
of atom labels and types, much like the output of Anton's nr2nametop, 
which I got later.  When I was done assigning the bond, angle and 
dihedral types, I changed atom labels back to numbers. The updated 
lig.itp is attached.

In the top file for the protein, after the #include ffG43b1 line, I inserted #include lig.itp. 

However, when I ran grompp with the new merged and renumbered top file, I *still* got the following message:

Fatal error: Invalid bond type 0

Per David's advice, I tried preparing the ligand alone for minimization, 
but grompp issued the same error message. There is no line number to 
point out where in the itp/top file things went wrong. With protein 
alone, everything goes well.

What exactly is going on here?

I will sincerely appreciate your help.

Martina

[ 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