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
>>>>> _______________________________________________
>>>>> 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
