Re: [AMBER] read trajectory using ambertools

From: Daniel Roe <>
Date: Mon, 15 Jul 2013 23:35:53 -0600

You can create a stripped topology file from the original topology
with cpptraj or parmed. You can actually modify the topology
on-the-fly in cpptraj, for example:

parm full.parm7
parmstrip :WAT

This will read in the full topology, strip water from it, then use the
stripped topology to read in trajectory


On Mon, Jul 15, 2013 at 9:40 PM, me, Nancy <> wrote:
> When I did the simulation, I used ntwprt>0 to set only the solute atoms
> output to the history file. So how to read this history file using cpptraj
> command with the parameter file including both solute and solvent atoms?
> Thanks.
> _______________________________________________
> AMBER mailing list

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 Mon Jul 15 2013 - 23:00:03 PDT
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