Besides cpptraj, You can use ncdump program (already in amber) to get any info (velocity, force, ...) you want.
Check ncdump ---help
Hai
> On Nov 17, 2016, at 4:39 PM, giulia palermo <giulia.palermo83.gmail.com> wrote:
>
> for using the information in an other code.
>
>
>
>
> 2016-11-17 12:58 GMT-08:00 Hai Nguyen <nhai.qn.gmail.com>:
>> just curious: why do you need to convert to human readable format?
>>
>> Hai
>>
>> On Thu, Nov 17, 2016 at 1:55 PM, giulia palermo <giulia.palermo83.gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I am trying to extract coordinates and velocities from the binary
>>> .rst7 file, which is produced from MD runs with AMBER, and converting
>>> it into a readable rst7 file.
>>> I have been using the follong command successfully with previous
>>> versions of AMBER (using ptraj). In the new version ptraj is
>>> substituted by cpptraj. However, the command should in principle work
>>> and provide me an rst7 file including coordinates and velocities.
>>> The coommand I am using is the following:
>>>
>>> cpptraj SYS.prntop <<EOF
>>> trajin SYS.rst7
>>> trajout SYS_new.rst7 RESTART
>>> EOF
>>>
>>> As a result, I obtain a file which only includes coordinates. However,
>>> I need the velocities, too.
>>>
>>> Can you please help me in getting it?
>>> The amber rst7, produced upon MD run, shoul contain the velocities,
>>> otherwise the MD engine would not be able to pursue dynamics.
>>> It seems a matter of how extract them in a readable (not binary) rst7
>>> format.
>>>
>>> Thank you very much
>>> Giulia
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Thu Nov 17 2016 - 15:30:02 PST
