[gmx-users] No default Proper [Bond, Angle, Dihedral]

[Arturas]

Hallo,

I got protein with prostetic group as a flavin. After grommp I've got
such a mess in an output (see below). Does it mean that my starting
structure have:
1. ill-defined geometry of flavin
2. ill-defined atom type in flavin
3. or it's just missing topology for flavin ??

Any suggestion. I am using defoult gromacs FF. Thanks in advance. Some
my heme proteins act similar way about heme.

...
creating statusfile for 1 node...
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1125 of the 1326 non-bonded parameter combinations
WARNING 1 [file "1gal.top", line 11554]:
  No default Bond types, using zeroes
WARNING 2 [file "1gal.top", line 11565]:
  No default Bond types, using zeroes
WARNING 3 [file "1gal.top", line 11567]:
  No default Bond types, using zeroes
WARNING 4 [file "1gal.top", line 30699]:
  No default Angle types, using zeroes
WARNING 5 [file "1gal.top", line 30700]:
  No default Angle types, using zeroes
WARNING 6 [file "1gal.top", line 33686]:
  No default Proper Dih. types, using zeroes
WARNING 7 [file "1gal.top", line 33687]:
  No default Proper Dih. types, using zeroes
WARNING 8 [file "1gal.top", line 33689]:
  No default Proper Dih. types, using zeroes
WARNING 9 [file "1gal.top", line 33691]:
  No default Proper Dih. types, using zeroes
WARNING 10 [file "1gal.top", line 33694]:
  No default Proper Dih. types, using zeroes
Cleaning up temporary file grompp4Ewjbj
Fatal error: Too many warnings, grompp terminated
 

Best wishes
Arturas Z.