Hi,
On Sat, Mar 19, 2016 at 6:04 AM Thomas Cheatham <tec3.utah.edu> wrote:
>
> ...Perhaps I missed the docs on this 20 year standard?
I referred to XDR as the 20-year old standard ;-)
> If we found this, would have made life easier in trying to match the
> awesome standards... -tec3
>
You're right, the GROMACS documentation doesn't make a normative statement
about TRR anywhere. Thanks, I will fix that.
Of course, people can talk to each other before launching into writing code
- thanks for the effort here, Daniel! :-)
Mark
> > On Mar 18, 2016, at 9:05 PM, Mark Abraham <mark.j.abraham.gmail.com>
> wrote:
> >
> > 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
> >>>
> >>>
> >>> _______________________________________________
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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 Sat Mar 19 2016 - 10:00:04 PDT
