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
Received on Fri Mar 18 2016 - 17:00:04 PDT
