[gmx-users] Error with "grompp"

[Justin Lemkul]

On 10/4/12 10:12 AM, Elie M wrote:
>
> Hello everyone,
> Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors:
> (1) ERROR 1 [file ffoplsaabon.itp, line 2692]:  Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
>
>
>
> (2) ERROR 2 [file ffoplsaabon.itp, line 2694]:  Not enough parameters

You should inspect ffoplsaabon.itp to see what is on these lines.  It is odd 
that grompp would complain about standard force field files if they have not 
been changed.

> and then a lot of errors of the type:
>
> ERROR 3 [file S54.top, line 118]:  No default Bond types
>
> ERROR 4 [file S54.top, line 120]:  No default Bond types
>
> ERROR 5 [file S54.top, line 124]:  No default Bond types
>
> ERROR 6 [file S54.top, line 127]:  No default Bond types.......
> Maybe the main question is for the third error is how to define these bond types and angles?

If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds 
that are not parameterized in the chosen force field) you need to add them 
either in ffbonded.itp (potentially dangerous, given the previous posts) or 
directly in the topology (probably safer).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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