[gmx-users] No default bond/angle/.. types

[Neva Besker]

Hi Gromacs users,

I'm new to gromacs. I'm trying to set up a system (cytochrome C) for
simulation. I did pdb2gmx with 3.0 version, because I had some problems
with Cys: I've modified CYS2 in pdb file but when I did pdb2gmx with 3.1.4
version for some reason the program did not read the file properly because
it thought that the residue type was CYSH rather than CYS2. Using pdb2gmx
of Gmx 3.0 everything is ok. After I made a grompp comand (3.1.4 version,
I need this one) and the system answered:


WARNING 1 [file "red1.top", line 1361]:
  No default Bond types, using zeroes
WARNING 2 [file "red1.top", line 1390]:
  No default Bond types, using zeroes
WARNING 3 [file "red1.top", line 4734]:
  No default Angle types, using zeroes
WARNING 4 [file "red1.top", line 4775]:
  No default Angle types, using zeroes
WARNING 5 [file "red1.top", line 6142]:
  No default Angle types, using zeroes
WARNING 6 [file "red1.top", line 6143]:
  No default Angle types, using zeroes
WARNING 7 [file "red1.top", line 6158]:
  No default Angle types, using zeroes
WARNING 8 [file "red1.top", line 6159]:
  No default Angle types, using zeroes
WARNING 9 [file "red1.top", line 6284]:
  No default Proper Dih. types, using zeroes
WARNING 10 [file "red1.top", line 6302]:
  No default Proper Dih. types, using zeroes


I'm using the output .top as well as the output .gro file from pdb2gmx to
give to grompp. The bond type that was not recognised was between SG of
CYS in the protein and CAB CR61 in HEME. I used the Gromos43a1 FF.
How can I solve the problem?
Thanks in advance.

Neva