On Thu, May 26, 2016 at 1:27 PM, Thomas C. Bishop <bishop.latech.edu> wrote:
> 1) Structure info: All provide same analysis (except Nastruct missing global
> axis and goovecalc(?))
The 'nastruct' command does not do global axis, but it does do the El
Hassan & Calladine groove width calculation - it just doesn't do it by
default (you need to specify 'groovecalc 3dna' as Hai mentioned). The
reason for this is to maintain backwards compatibility with older
'nastruct' input (the default is to do P-P and O4-O4 distances).
> 2) All can do "automatic" base pair recognition (curves too?)
> 3) 3DNA and Curves allow manually assigning the base pairs
> 4) ONLY nastruct (via cpptraj can read traj, crd, pdb , AND dcd)
Cpptraj also reads mol2, binpos, trr, cif, etc.
> 5) statistics:
> Curves comes /w Canal for statistical analysis and propery handles circular
> averaging
> nastruct can use cpptraj data analysis commands
The averaging in cpptraj also takes into account periodicity. The only
caveat is if you are reading in data that is periodic you need to mark
it as such (or specify 'torsion' when using the 'avg' analysis
command).
> 3DNA (roll your own stats?)
> 6) rebuilding ?
> I'm less certain about rebuilding atomic or coarse grained models
> 3DNA yes no limits on length of model... atomic and cg models can be built
> nastruct: ??? w/ arbitrary parameters and sequence?
> Curves?
> 7)limits:
> 3DNA: I've used 3DNA to make very very long models and analyze them; NO
> SOURCE CODE
> CURVES: hard coded for ~150bp but SOURCE provided so recompiled as you see
> fit
> NASTRUCT: source? limits?
Source is freely available as part of AmberTools or via GitHub:
https://github.com/Amber-MD/cpptraj
The only limits for cpptraj as far as I know is available system
memory. Of course, 'nastruct' doesn't do any model building so that
may not be relevant to your point.
Let me know if you have more questions.
-Dan
>
> On 05/26/2016 09:09 AM, Vlad Cojocaru wrote:
>
> 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
> Vlad
>
> 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
> [1]www.latech.edu/~bishop
> ********************************
>
> --
> 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]mpi-muenster.mpg.de
> [2]http://www.mpi-muenster.mpg.de/43241/cojocaru
>
> --
> *******************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> [3]www.latech.edu/~bishop
> ********************************
>
> References
>
> 1. http://www.latech.edu/%7Ebishop
> 2. http://www.mpi-muenster.mpg.de/43241/cojocaru
> 3. http://www.latech.edu/~bishop
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Fri May 27 2016 - 08:30:02 PDT
