[gmx-users] Orientation restraints

[Miguel Ortiz-Lombardia]

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
http://ndbserver.rutgers.edu/ftp/NDB/programs/freehelix98/

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.

Cheers,



Miguel

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
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- --
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
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