On Tue, Aug 23, 2016 at 3:23 PM, Samuel Bowerman
<sbowerma+amber-l.hawk.iit.edu> 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 (http://archive.ambermd.org/201504/0141.html)
> 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 All.nc name A
# Strip everything but A from COORDS set A
crdaction A strip !<mask for A>
# Repeat for B
loadcrd All.nc name B
crdaction B strip !<mask for B>
# Repeat for C-J
loadcrd All.nc name CJ
crdaction CJ strip !<mask for C-J>
# Combine
combinecrd B A CJ crdname Reorder
# Write out
crdout Reorder Reorder.nc
Haven't tested the above but I think it will work. Hope this helps,
-Dan
>
> 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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--
-------------------------
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 Fri Aug 26 2016 - 14:00:03 PDT
