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

David spoel at xray.bmc.uu.se
Wed Jun 16 16:54:54 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
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.

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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