Hello,
NetCDF is a file format specification. Amber is able to use this format
for various purposes. As of Amber 12, I am aware of trajectory files as
well as restart files that can be read and written as NetCDF files.
From what you have written so far, it is not entirely clear what you
want to convert to what.
For your understanding, two examples:
It is possible to load a NetCDF trajectory file with cpptraj via the
trajin command and select only one single frame for further processing.
You can then save the atomic coordinates of this frame in the classical
Amber ASCII format (as 'crd' file) using the trajout command.
Likewise, if a NetCDF restart file is your input, you can use cpptraj to
create a an ASCII restart file from it.
In any case, the AmberTools manual is your friend here.
Hope this helps,
Jan-Philip
On 07/16/2013 11:46 AM, Yip Yew Mun wrote:
> Okie, then is it possible to convert NetCDF files to crd files in cpptraj? If so, how can I go about doing it?
>
> Thanks
>
> Regards
> Yip Yew Mun
> Graduate, PhD
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
> On 16-Jul-2013, at 5:41 PM, Daniel Sindhikara wrote:
>
>> For AMBER they store essentially the same data.
>>
>> NetCDF are compressed binary files.
>> .crd files are plain text.
>>
>> NetCDF take up much less space and are faster to read/write (and are
>> recommended).
>>
>>
>>
>>
>> On Tue, Jul 16, 2013 at 6:24 PM, #YIP YEW MUN# <YIPY0005.e.ntu.edu.sg>wrote:
>>
>>> Hi, I wish to ask what's the difference between NetCDF files and .crd
>>> files?
>>>
>>> --
>>> Regards
>>> Yip Yew Mun
>>> Graduate, PhD
>>> Chemistry and Biological Chemistry
>>> School of Physical and Mathematical Sciences
>>> Nanyang Technological University
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
>> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
>> sindhikara.gmail.com <http://www.dansindhikara.com>
>> --
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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 16 2013 - 03:30:02 PDT
