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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Received on Thu Mar 17 2016 - 17:30:07 PDT
