Re: [AMBER] Deleting Box info from trajectory

From: Daniel Roe <>
Date: Sat, 14 Jun 2014 15:27:11 -0600


Keeping in mind everything that Dave said, if you still need to remove box
info from a topology you can do it with cpptraj like so:

parm input.parm7
parmbox nobox
parmwrite out output.parm7


On Sat, Jun 14, 2014 at 2:09 PM, Kshatresh Dutta Dubey <>

> Dear Users,
> I have a simulated a protein ligand complex using PBC, but for the
> purpose of QM/MM calculations I want to remove the box info from the
> trajectory 'without striping water'. I know that using cpptraj/ptraj we can
> modify the box info but I fear that it will demand new prmtop file without
> box info for any further analysis of no-box trajectories. If I am
> generating a new prmtop file without box info, I guess it will not match
> no. of atoms ( since I am not striping water). I will be grateful if
> someone suggests me any idea to remove PBC info without re-running new
> simulations, for QM/MM calculations.
> Regards
> Kshatresh
> _______________________________________________
> 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) 585-6208 (Fax)
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Received on Sat Jun 14 2014 - 14:30:02 PDT
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