[gmx-users] Dummies in .rtp and topology for sp-hybrid atom

[=?koi8-r?Q?=22?=Alexander Terehov=?koi8-r?Q?=22=20?=]

I am posting this message again and I hope someone will answer me...

>
> On Wed, 2004-06-16 at 15:54, =?koi8-r?Q?=22?=Alexander
> Terehov=?koi8-r?Q?=22=20?= wrote:
> > I am trying to add a description of a molecule to OPLS-AA force field and
recently I've found that one of its nitrogens is most likely sp-hybrid, that
means 180-degree angle between its two bonds and orthogonal location of two
planar pi-systems it is involved in. Is it possible to produce an appropriate
topology in such case?
> >
> you mean
>
> Ring == C == Ring
> ?

Like this. But with N and two pi-systems orthogonal to each other:

plane_1 - N = plane_2

N is really sp with two bonds on one line.

> You can do linear systems with dummies. If the rings are in the same
> plane you may have to add some weird impropers as well.
>

Sorry, I am not very familiar with Gromacs soon... I have to describe my
structure as a new protein residue (an entry in .rtp file). AFAIK, it is not
possible to make things like [dummies3] in such case... How can I use dummies
anyway?


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