[gmx-users] Orientation restraints

Miguel Ortiz-Lombardia molatwork at yahoo.es
Tue Apr 11 21:37:55 CEST 2006

Hi Bob,

Just a comment: if you don't have a homogeneous DNA sequence (and
perhaps even in such a case) you will probably end distorting the
sugar-phosphate backbone of the DNA if forcing every base pair to be
normal to a common z-axis.

Anyway, look for one of these two programs:

freehelix (by Dickerson) at

curves (by Lavery and Sklenar) at http://www.ibpc.fr/UPR9080/Curindex.html

They both have approached the problem you're describing among other
structural descriptions/analysis of DNA.



En/na Bob Johnson ha escrit:
> Hello everyone,
> My system consists of DNA and a carbon nanotube. I would like to restrain the
> DNA bases in a way that the plane formed by each base is parallel to the
> z-axis. In other words, I would like to orient the bases such that the normal
> of each plane is perpendicular to the z-axis. I don't think using angle
> restraints is sufficient for what I want to do because there you can only
> restrain pairs of atoms. Any ideas how I could define a normal vector to each
> plane and have that maintain a 90 degree angle with respect to the z-axis?
> Thanks,
> Bob Johnson
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: molatwork at yahoo.es
- ----------------------------------------------------------------------
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
                                                Blaise Pascal, Pensées

More information about the gromacs.org_gmx-users mailing list