On Thu, May 26, 2016 at 8:09 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> 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 ....
Just to be clear, cpptraj can calculate all NA structural parameters
*except* global helical axis stuff. It's been on my to-do list for a
while...
-Dan
>
> 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
>> 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
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Thu May 26 2016 - 07:30:03 PDT
