[gmx-users] Help - No default Bond types dna

Ragnarok sdf fabracht1 at gmail.com
Fri Aug 22 03:58:20 CEST 2008

Hello. Ie been trying to run a DNA simulation with gromacs using amber99
force field. I've started with my DNA sequence complexed with the protein,
but then decided to separate them to know exactly what the problem was. Now
I am not even using the DNA sequence from my pdb file. I`ve used the NAB
server to create a DNA sequence which is exactly the same as the one I had.
I decided to do this in order to minimize the problems with the amber
forcefield. Well, that didn't work either.
I keep getting the "Error - No default Bond types.....no default angle
types....etc "
On a previous email I asked the same question, and the answer was. Take a
look at the lines where the error appears. Just to be more specific on my
problem.....ERROR 0 [file "1vkxdna_C.itp", line 71]:
  No default Bond types
ERROR 0 [file "1vkxdna_C.itp", line 196]:
  No default Angle types
Ok. I've taken the last advice and went ther to line 196. Except that on
line 196 there are 4 columns
"16    18    19     1"  with values that I cannot spot the problem. I went
to the manual to see what each line means but came out without knowing
exactly what to do with them.
Another problem I've spotted is that the charge (no matter what i try)
always comes out as a non integral value. I've renamed all atoms exactly
like they should be...one by one....really...one by one.
I would like some advice on the problem if possible.

Ps: The amber Dickerson test works out just fine.
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