Hi,
The GROMACS TRR format is based on XDR, which is defined to be a big-endian
format in a 20-year-old IETF standard. I think there is no good reason to
write a tool to be able to write non-confoming XDR, and so no reason for
any tools to be able to read such files. I also think we have better things
to do than rippling "please support little-endian TRR" requests to all the
different software packages that might handle such files! :-)
Cheers,
Mark
On Sat, Mar 19, 2016 at 12:33 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Turns out this is may be a bug (feature?) in Gromacs analysis tools.
> By default cpptraj writes out TRR trajectories as little endian on
> little endian architecture. However, it seems that Gromacs analysis
> tools expect TRR trajectories to be big endian. I've added a flag to
> the GitHub beta version of cpptraj
> (https://github.com/Amber-MD/cpptraj), 'bigendian', that you can use
> with 'trajout' to force writing a big endian trajectory. I've tested
> it and it works for me - I'd be interested if it works for you as
> well.
>
> -Dan
>
> On Thu, Mar 17, 2016 at 6:18 PM, Dr. Robert Molt <rwmolt07.gmail.com>
> wrote:
> > Good to know I am not being dense! Happy it is reproducible.
> >
> > On 3/17/2016 8:09 PM, Daniel Roe wrote:
> >> I've been able to reproduce this issue and I'm currently working on it.
> >> Thanks for bringing it to my attention! I'll let you know when I have a
> >> fix.
> >>
> >> -Dan
> >>
> >> On Thursday, March 17, 2016, Dr. Robert Molt <rwmolt07.gmail.com>
> wrote:
> >>
> >>> Good evening,
> >>>
> >>> Pardon the delay; writing minor codes.
> >>>
> >>> I have been using Amber14. The error from do_x3dna was a segmentation
> >>> fault; it could not read a single frame. I am happy to assist in any
> way
> >>> I can, I am appreciative of all the support Amber gives via this forum.
> >>>
> >>> On 3/17/2016 9:37 AM, Daniel Roe wrote:
> >>>> 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
> >>> <javascript:;>> 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 <javascript:;>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org <javascript:;>
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org <javascript:;>
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >
> >
> > _______________________________________________
> > 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 Fri Mar 18 2016 - 21:30:03 PDT
