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

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 22 12:09:30 CEST 2008

Ragnarok sdf wrote:
> 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.

The listing there are the three atoms in the angle (ai, aj, ak) and the function 
type.  Descriptions of these are in Chapter 5 of the manual.  Details are a bit 
sparse regarding angles, but the text regarding other parameters and topology 
format are more detailed, and generally applicable.

Other lines within the [ angles ] section should have angle parameter 
information following the fourth column, but that line will not.  Determine if 
there should be, or if something else has gone wrong (see below).

> 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.

Then something probably went wrong with topology creation, but that's very hard 
to diagnose.  Each residue (nucleotide) in the .top should end with an integer 
charge (;qtot in the .top).  See if this is breaking down, and if so, post one 
of the nucleotides on the list if you can't find out what's wrong with it.

Also, please post your pdb2gmx command line from when you created the .top.


> Ps: The amber Dickerson test works out just fine.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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