[gmx-users] Is it possible to write topology for sp-hybridnitrogen ?

=?koi8-r?Q?=22?=Alexander Terehov=?koi8-r?Q?=22=20?= al_terehov at mail.ru
Fri Jun 18 18:23:38 CEST 2004

> 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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