RFC 4506?
________________________________________
From: Thomas Cheatham [tec3.utah.edu]
Sent: 19 March 2016 05:04
To: AMBER Mailing List
Subject: Re: [AMBER] GROMACS File Conversion Subtlety
...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:;>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 19 2016 - 01:00:03 PDT
