Re: [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory

From: Jason Swails <>
Date: Mon, 16 Dec 2013 08:11:05 -0500

On Mon, 2013-12-16 at 13:22 +0800, #YIP YEW MUN# wrote:
> Hi, I produced a trajectory of a full protein, and then I truncated certain
> parts of the protein in the trajectory using ptraj. How can I generate the
> new prmtop file for this new truncated-protein trajectory?

You can use either ParmEd or cpptraj to create a corresponding topology
file. Look at either the "strip" command (in ParmEd) or the "parmstrip"
command in cpptraj.

In fact, you can do this in cpptraj in a single step when you use the
"strip" command to remove part of the system. The "outprefix" keyword
will create a matching topology file. For example:

cpptraj << EOF
parm full_system.parm7
strip :100-999999 outprefix trunc
trajout netcdf

The above command will remove all atoms in residue 100 and higher and
create a new NetCDF trajectory called as well as a topology
file called trunc.full_system.parm7.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 16 2013 - 05:30:02 PST
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