Re: [AMBER] cpptraj + nastruct

From: Vlad Cojocaru <>
Date: Thu, 26 May 2016 09:33:52 +0200

Dear Tom,

We are using Curves or X3DNA to do this type of analysis. These programs
recognize automatically the base pairs and give you all data you need
regarding the DNA helix. As I don't have experience with nastruct in
Cpptraj, I cannot say if the functionality is as good as in these 2
programs but as these 2 were made especially for this type of analysis,
I'd expect the functionality is superior to Cpptraj which is a more
general analysis tool. But sure, I may be wrong ...

Best wishes

On 05/26/2016 01:31 AM, Thomas C. Bishop wrote:
> Dear Amber,
> I'm using CPPTRAJ to analyze some simulations w/ dsDNA and want to extract
> helical parameter data w/ nastruct.
> Is there any other method than using a reference structure for having
> nastruct identify the base pairs.
> Specifically can I tell nastruct which residues are paired with which?
> Pointers to tools for statistically summaries of the results would be much
> appreciated.
> Thanks in advance,
> Tom

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
AMBER mailing list
Received on Thu May 26 2016 - 01:00:02 PDT
Custom Search