Re: [AMBER] Amber nc trajectory file analysis by x3dna

From: Maria Nagan <>
Date: Fri, 31 Jul 2020 11:22:17 -0400

Hi Jenny,

Technically this would be a question for the x3dna forum ( <>) as it pertains to what x3dna will allow.

It’s been a while since I’ve done 3dna analysis but if I remember correctly, you need to convert everything to pdb files and then script it to read into 3dna. So you’d need to do use cpptraj to take your netcdf file and make it into pdb files.

Alternatively, you could also try this (haven’t used it) and modify it for your netcdf file — do_x3dna. <>

Also, you might try the nucleic acid analysis (nastruct) in cpptraj (see Amber 2020 Manual page 679) and this tutorial on nucleic acids written by Rodrigo <>.

Maria Nagan, PhD
Chemistry Department
Stony Brook University
Stony Brook, NY 11794

> On Jul 31, 2020, at 11:05 AM, Jenny 148 <> wrote:
> Dear all,
> I have a 500ns trajectory file of a dna duplex, which I would like to
> analyze using x3dna package. Since I do not know much about this, could
> someone let me know about the procedure for the analysis of the same??
> Could we directly analyze the nc file in x3dna ?
> Thank you
> Jenny
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Received on Fri Jul 31 2020 - 08:30:03 PDT
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