Re: [AMBER] cpptraj - atomicfluct

From: Daniel Roe <>
Date: Tue, 16 Sep 2014 08:30:36 -0600

On Mon, Sep 15, 2014 at 7:47 PM, Thomas Cheatham <> wrote:
> ...there is not an easy way to have ptraj/cpptraj output "residue" numbers
> as you see fit. It simply outputs x-axis that are numbered 1->N for the
> select groups (either byres or bynum, still numbered 1->N based on the
> selection and NOT matched to atom/residue numbers).

While this is true for ptraj, cpptraj should print the residue number
on the x axis when 'byres' is used. For example for the command
"atomicfluct :190-210 byres out afluct.dat" you should get output like

#Res AtomicFlx
     190 0.4262
     191 0.4674
     192 0.4924
     193 0.6178
     194 0.5013

The same is true for atom numbering (i.e. it takes the mask into
account). If you are not getting this, you're probably using an old
version of cpptraj and should upgrade to the latest from Amber 14
(with all updates applied).


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)
AMBER mailing list
Received on Tue Sep 16 2014 - 08:00:03 PDT
Custom Search