Re: [AMBER] cpptraj + nastruct

From: Vlad Cojocaru <>
Date: Thu, 26 May 2016 16:09:51 +0200

Hi Tom,

For Curves you also need a conversion to amber ASCII trajectories, so
its also not perfect from that point of view .. I don't know how large
and how many are your trajectories, but I did not see a major time
limitation by having a temporary conversion to ASCII trajectories during
an automated workflow that ultimately runs Curves on these ASCII mdcrd
file (deleting them afterwords)...

But, sure, I see the point that if cpptraj can do everything in one
step, it will be more efficient .. Maybe I should also give it a try
....especially as Daniel mentioned it can actually do everything Curves
does ....

Best wishes

On 05/26/2016 02:49 PM, Thomas C. Bishop wrote:
> Good to hear from you Vlad.
> I had been using X3DNA but last I checked 3DNA could not read DCD's
> only pdbs so processing is slow.
> ( I have some vmd scripts that automate 3DNA analysis if anyone's
> interested... but it's not terribly efficient)
> We tested cpptraj yesterday and I was _amazed_ at how fast it is
> compared to 3DNA.
> cpptraj has advantage over Curves/3DNA that it can do a lot of
> analysis in one run.
> I still need to compare to what Curves offers.
> Cheers,
> Tom
> On 05/26/2016 02:33 AM, Vlad Cojocaru wrote:
>> 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
>> Vlad
>> 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
> --
> *******************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> ********************************

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]
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Received on Thu May 26 2016 - 07:30:02 PDT
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