Thanks for the suggestions. As some of the software in my lab still relies on .mdcrd files, I was wondering if it's possible to convert NetCDF files to .mdcrd files. =)
Sent from my iPad
On 16 Jul, 2013, at 6:09 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote:
> 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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>>
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Received on Tue Jul 16 2013 - 03:30:03 PDT
