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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 24 Nov 2014 08:26:46 -0700

On Sun, Nov 23, 2014 at 6:42 PM, Jason Swails <jason.swails.gmail.com> 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
unstrip
strip :1-50 outprefix Protein2
outtraj Protein2.rst7

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

-Dan

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