Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box

From: Daniel Roe <>
Date: Sun, 10 Feb 2013 19:58:03 -0700


You can strip atoms and generate a corresponding prmtop with cpptraj
in one step. Also, if you specify 'nobox' you're getting rid of box
information (which it sounds like you want to keep) from your
coordinates, so I would remove that keyword. For example:

parm prmtop
trajin wb_lambdaN_100.crd
strip :WAT&!(:50000-155000) outprefix strip
trajout wb_strip_lambdaN_100.crd

will strip the desired atoms, write out a stripped trajectory
(wb_strip_lambdaN_100.crd) and write out the corresponding topology
(strip.prmtop). You can do the same thing with the 'closest' command:

parm prmtop
trajin wb_lambdaN_100.crd
closest 105000 <solute mask> outprefix closest
trajout wb_closest_lambdaN_100.crd

will retain the closest 105000 solvent molcules to your solute mask,
writing out the corresponding topology as closest.prmtop.

As Jason said, if you do decide to strip your systems in this way you
need to equilibrate them very carefully, especially when using the
'strip' command as you may end up with pockets of vacuum in your

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sun Feb 10 2013 - 19:30:03 PST
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