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> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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)
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 30 2016 - 13:00:03 PDT
