Hi,
On Fri, Mar 18, 2016 at 10:04 PM, Mark Abraham <mark.j.abraham.gmail.com> wrote:
> 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
That's good to know, although I was not able to find any clear
documentation to this effect. For example, the first couple of results
of a google search for "gromacs trr file format description" indicate
no clear link between the XDR format and gromacs TRR files (although
the fourth hit, a link to MDAnalysis documentation, starts to hint at
this indirectly via the way the modules are named, but even then it's
not clear). Compare this to the first result of a google search for
"amber netcdf file format description", which for me is
http://ambermd.org/netcdf/nctraj.pdf.
Now that I know that TRR should be XDR I will make the appropriate
updates in cpptraj, although it does seem strange to me to have a
big-endian format in what is primarily a little-endian world! Thanks,
-Dan
> 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
>> >>>>
>> >>>
>> >>> _______________________________________________
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>> >>>
>> >>
>> >
>> >
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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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--
-------------------------
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 - 07:30:03 PDT
