Hm - sounds like a potential bug. Would you mind sending me off-list some
files I could use to reproduce this behavior (sounds like trajectories only
need to be 2 frames to see the problem).
I am currently in the middle of a move so I may not be able to get to this
as soon as I would like, but if there is a problem I'd eventually like to
correct it.
Glad to hear you could still do the analysis you wanted.
-Dan
On Tuesday, August 30, 2016, Samuel Bowerman <sbowerma+amber-l.hawk.iit.edu>
wrote:
> Hi Dan,
>
> Thanks for your response. While I agree that what you've posted *should*
> work as is, it unfortunately does not. The first frame of the trajectory
> is reordered appropriately, but subsequent frames are riddled with strange
> atom configurations: for example, the atoms within C-J get lumped into a
> giant ball instead of being mapped to their original locations. I am not
> too familiar at working with trajectories as COORDS sets, so I can't offer
> a guess as to why this may be occurring.
>
> That being said, my most pressing need is to use cpptraj to identify
> different structural clusters in groups A and B, so I've decided to just
> strip my data to these groups and then use atommap on the resulting
> trajectories prior to clustering. While being able to use a wider variety
> of cpptraj's utilities on the full simulations would be fantastic, this
> will satisfy my original plans for these trajectories.
>
> Thanks again for your assistance.
>
> Take care,
> Samuel Bowerman
> Ph.D. Candidate
> Department of Physics
> Illinois Institute of Technology
>
> On Fri, Aug 26, 2016 at 3:40 PM, Daniel Roe <daniel.r.roe.gmail.com
> <javascript:;>> wrote:
>
> > On Tue, Aug 23, 2016 at 3:23 PM, Samuel Bowerman
> > <sbowerma+amber-l.hawk.iit.edu <javascript:;>> 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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> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > 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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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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 Wed Aug 31 2016 - 06:30:03 PDT
