[gmx-users] endcapping

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
> 
> (1) The amide isn't completely planar (which it should be)
> CA <-> C <-> NH2 lie in the same plane, but the O is flipped 30 degrees.
> This is not a very big problem, but is there something I could do about
> it?
> 
> (2) grompp gives the error:
> Warning 1 [file "2mlti.top", line 1404]:
>   No default Angle types, using zeroes
> 
> Should this worry me?

In principle, yes. This means you ended up with a unknown
combination of atom types in one of the angle definitions.
Maybe you have a wrong atom type somewhere. THis might well
be the cause of your 30 degree O out of plane, which sounds
like a tetrahedral orientation around the carbon atom (like
you would have around CA), i.s.o. a planar one...

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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