[gmx-users] Help with grompp with amber99 forcefield

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 19 19:54:31 CEST 2008

Ragnarok sdf wrote:

> And the second error is the total system carge which is a non integral 
> charge.
> I've looked for  the " ERROR 0 [file "1VKX_C.itp", line 420]:
>   No default Bond types" solution but no one seams to have had the same 
> problem as I.

Not entirely true, they just haven't had the exact same quote :)  If, for 
example, you search "No default bond types," you return 91 results.

Bottom line is your topology is badly broken.  If you look at line 420, etc. in 
your topology, you should be able to identify the atoms that grompp is trying to 
bond.  You may find some unexpected behavior.  Are you using the Amber ports? 
If so, there are some very specific instructions on how to deal with DNA, as 
several files need to be modified to give correct terminal nucleotides:


The missing bonds might be related to the non-integral charge - there are 
fragmented molecules or incorrect atom types.

Careful inspection of the topology should lead you to a solution.


> I believe the charge problem can be found in the users list, so the 
> actual doubt lies in the first problem.
> Thank you in advance
> Fabrício Bracht
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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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