Hi Robert,
Thanks for bringing this to my attention. I don't often work with
gromacs files so it's certainly possible there is some issue with
cpptraj-generated trr files. I have checked them with VMD as well and
found no probelsm (i.e. vmd reads cpptraj-generated trr files just
fine) so its likely something subtle with the format as you suggest.
What version of cpptraj did you run this with? And can you provide any
more details on what the error was (exact message(s), segfault, etc)?
I'll look into this and see what I can find.
-Dan
On Thu, Mar 17, 2016 at 12:03 AM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good morning,
>
> I believe I have encountered a bug of sorts in converting an Amber
> trajectory to a GROMACS format...but it's unusual and perhaps very
> limited in its inconvenience.
>
> I converted an Amber trajectory to GROMACS style via cpptraj:
>
> parm name_change.prmtop
> trajin full_no_waters.mdcrd 49990 last 1
> autoimage
> trajout Equilibrated trr
> go
> quit
>
> I can generate a .gro file via the ParmEd version being developed
> currently by Jason Swails on github. When I visualize this in VMD, it
> looks just fine. This is my only meaningful way to check that it works
> correctly, and it passes just fine.
>
> However, when I apply this trajectory to be analyzed using do_x3dna (a
> software developed for analyzing GROMACS trajectories), it fails. After
> consulting with the developer of the do_x3dna software, I find that he
> confirms the trajectory is corrupt in some sense. I eventually tried
> converting the trajectory via VMD, instead of cpptraj, and it worked
> just fine in do_x3dna. The do_x3dna developer confirms using a
> "normally" generated GROMACS .trr file (meaning not coming from Amber,
> originally) works fine.
>
> I do not mean to claim that the conversion in cpptraj does not work most
> generally; it obviously worked fine for me when I checked it visually in
> VMD. Moreover, I am sure this underwent more exhaustive testing that I
> can appreciate. But in some quality, the conversion does not seem to work.
>
> VMD works, but using a GUI is slow (I have many large trajectories). I
> am going to begin experimenting with
>
> http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion
>
> by the esteemed Dr. Lemkul to find a way to do this on the command line.
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
>
> _______________________________________________
> 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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Received on Thu Mar 17 2016 - 07:00:03 PDT
