[gmx-users] [Fwd: problem with URA residue in ffgmx]

[K.A. Feenstra]

> From: John Kerrigan <kerrigje at UMDNJ.EDU>
> 
> Help, pretty please?  I am working on an RNA model using the Gromacs 87
> force field (ffgmx.rtp).  I solvate the RNA and am cruising along fine until
> I grompp the system in preparation for energy minimization.  I have multiple
> instances of the following error:
> 
> No default Angle types, using zeroes
>
[..snip..]
>
> I see this same error in versions 3.1.2 (windows) and 3.1.4 (unix).  Any
> suggestions?

What I know about DNA is that it is only marginally supported in Gromacs
at all (e.g. termini generation in pdb2gmx is hardly functional), and that
even the forcefield is not as well-wrought as it probably should be for
serious work. 

Having said that, I see no problem in simply adding the missing angle
parameters to the forcefield (especially seeing the mediocre quality
of the DNA parameters anyway...). Simply choose parameters that seem
appropriate from analogy with similar groups. If you feel that some
of them are rather critical, you should check against an independent
source - preferably experimental data, e.g. X-ray crystallographic
coordinates, or any other that you would feel are appropriate and can
actually be reliably extracted from a simulation. A note of caution:
this is the field of forcefield development, which is neither trivial
nor very exciting (IMHO...), just tedious.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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