Re: [AMBER] Problem with atommap function in cpptraj (v16)

From: Daniel Roe <>
Date: Fri, 26 Aug 2016 16:40:24 -0400

On Tue, Aug 23, 2016 at 3:23 PM, Samuel Bowerman
<> wrote:
> If I inspect the atommap.dat file, then I get the expected Target <->
> Reference index mapping for fragments 1 and 2, but fragments 3 through 10
> are filled with "--- ---" for target indices and names. I believe this
> may be a result of those fragments not requiring mapping, but I have also
> found a two-year old thread (
> that mentioned system size potentially being an issue - my system is
> roughly 30,000 atoms.

Oh boy - yeah that's way bigger than any system I've tested 'atommap'
on. It was originally developed to re-map small drug-like molecules. I
don't remember offhand but I think the largest I ever tested on was
about 128 atoms or so. I could probably enhance the performance a lot
by doing things on a per-residue basis but there was no real demand
for it when I was originally writing the code and unfortunately I
haven't had a lot of free time.

If the fragments themselves are contiguous and all that has changed is
the ordering, i.e. the original is:

A B C ...

and the new order is

B A C ...

what you might be able to do is manually reorder whichever trajectory
(or trajectories) are shortest via 'strip' and 'combinecrd'. For
example, say I wanted to reorder the first to match the second. I
would do something like this (I'm oing to use COORDS data sets so I'm
assuming you have enough memory):

parm All.parm7
# Load entire trajectory as COORDS set A
loadcrd name A
# Strip everything but A from COORDS set A
crdaction A strip !<mask for A>
# Repeat for B
loadcrd name B
crdaction B strip !<mask for B>
# Repeat for C-J
loadcrd name CJ
crdaction CJ strip !<mask for C-J>
# Combine
combinecrd B A CJ crdname Reorder
# Write out
crdout Reorder

Haven't tested the above but I think it will work. Hope this helps,


> If anyone could suggest an explanation, a fix, or a work-around for this
> problem, I would greatly appreciate it. Thanks!
> Take care,
> Samuel Bowerman
> Ph.D. Candidate
> Department of Physics
> Illinois Institute of Technology
> _______________________________________________
> AMBER mailing list

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 Fri Aug 26 2016 - 14:00:03 PDT
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