https://xkcd.com/927/
On "standards"
On 3/19/2016 1:04 AM, Thomas Cheatham wrote:
> ...Perhaps I missed the docs on this 20 year standard? If we found this, would have made life easier in trying to match the awesome standards... -tec3
>
>> 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:;>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> 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 Fri Mar 18 2016 - 22:30:05 PDT
