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
[1]www.latech.edu/~bishop
********************************
References
1. http://www.latech.edu/~bishop
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Received on Thu May 26 2016 - 06:00:02 PDT
