Re: [AMBER] extracting velocities from rst7 file

From: Hai Nguyen <>
Date: Thu, 17 Nov 2016 15:58:09 -0500

just curious: why do you need to convert to human readable format?


On Thu, Nov 17, 2016 at 1:55 PM, giulia palermo <>

> 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
> 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
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Received on Thu Nov 17 2016 - 13:00:05 PST
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