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

From: Samuel Bowerman <sbowerma+amber-l.hawk.iit.edu>
Date: Tue, 23 Aug 2016 14:23:56 -0500

Hello AMBER community,

I have run into a problem with the "atommap" command of cpptraj. My system
is contained in 10 fragments, but I had to swap the order of fragments 1
and 2 for simulation with an external program. My plan for analysis
requires combining the reordered simulation with a previous run in which
fragments 1 and 2 were not switched by using "atommap". However, when I
run the command, I receive the following warning:

"Warning: AtomMap: Not all atoms were mapped. Frames will not be modified."

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 (http://archive.ambermd.org/201504/0141.html)
that mentioned system size potentially being an issue - my system is
roughly 30,000 atoms.

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
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Received on Tue Aug 23 2016 - 12:30:02 PDT
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