Hi,
I was able to track down the bug - in 'crdaction' where the action
modified the topology, the wrong frame was being passed in leading to
memory issues. I've fixed the issue in GitHub and will work on a patch
for AmberTools. If you use the GitHub version the script previously
posted should work fine now. Thanks for the report and the files!
-Dan
On Wed, Aug 31, 2016 at 9:12 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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>
>> 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)
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > 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)
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Sep 20 2016 - 07:30:02 PDT
