Okie, thanks.! =D
Sent from my iPad
On 16 Jul, 2013, at 6:25 PM, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> Hi,
>
> Yes, NetCDF to mdcrd conversion possible and easy (with cpptraj and
> ptraj). Just check the AmberTools manual and the trajin / trajout
> commands.
>
> --Marc
>
> On 16 July 2013 11:19, Yip Yew Mun <yipy0005.gmail.com> wrote:
>> 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
>>>>>> _______________________________________________
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>>>>>> 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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Received on Tue Jul 16 2013 - 04:00:03 PDT
