[AMBER] extracting velocities from rst7 file

From: giulia palermo <giulia.palermo83.gmail.com>
Date: Thu, 17 Nov 2016 10:55:59 -0800

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

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Received on Thu Nov 17 2016 - 11:00:02 PST
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