Re: [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files?

From: Daniel Roe <>
Date: Mon, 24 Nov 2014 08:26:46 -0700

On Sun, Nov 23, 2014 at 6:42 PM, Jason Swails <> wrote:
> You can use cpptraj or ParmEd to strip out a portion of the system and write another prmtop file.

FYI, the corresponding cpptraj script is:

parm combined.parm7
trajin combined.rst7
strip :51-90 outprefix Protein1
outtraj Protein1.rst7
strip :1-50 outprefix Protein2
outtraj Protein2.rst7

This will also work if you need to strip trajectory files.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Nov 24 2014 - 07:30:03 PST
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