[gmx-users] PROBLEM WITH GROMOS96ff

[Chiara Bello]

Dear Gromacs Users,
I'm doing a simulation of a ligand using GROMOS96 54a7 force field with the 4.6.5 VERSION.
I added the residue to the .rtp file and to residuetypes.dat, after that I run my .gro file on pdb2gmx and subsequently on genbox but they gave me a .top file in which the ga_xx keys are missed only for the angles between alifatic carbon atoms and H atoms. 
This is a problem when I try to add ions using grompp because it gives me the following errors:

[...]
ERROR 88 [file test.top, line 620]:
  No default G96Angle types


ERROR 89 [file test.top, line 630]:
  No default Proper Dih. types


ERROR 90 [file test.top, line 631]:
  No default Proper Dih. types


ERROR 91 [file test.top, line 635]:
  No default Proper Dih. types


ERROR 92 [file test.top, line 638]:
  No default Proper Dih. types


ERROR 93 [file test.top, line 663]:
  No default Proper Dih. types

NOTE 3 [file test.top, line 750]:
  System has non-zero total charge: 5.350000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  

There were 3 notes

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1610

Fatal error:
There were 93 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


Topology file is presented as follows:

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     2 
    2     1     4     2 
    2     1     5     2 
    3     1     4     2 
    3     1     5     2 
    4     1     5     2 
    1     5     6     2 
    1     5     7     2    ga_15
    1     5    11     2    ga_15
    6     5     7     2 
    6     5    11     2 
    7     5    11     2    ga_15
    5     7     8     2 
    5     7     9     2 
    5     7    10     2 
    8     7     9     2 
    8     7    10     2 
    9     7    10     2 
    5    11    12     2 
    5    11    13     2 
    5    11    14     2    ga_15
   12    11    13     2 
   12    11    14     2 
   13    11    14     2 
   11    14    15     2    ga_27
   11    14    19     2    ga_27
   15    14    19     2    ga_27
   14    15    16     2    ga_25
   14    15    17     2    ga_27
   etc...

Where the first lines match to H - C(sp3) - H and H - C(sp3) - C(sp3) angles.
I think that angles must be definited in the force field because they are present also in Alanine and other aminoacids. Is this a problem of my protocol or a bug?
Thanks in advance,
Chiara.