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> 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
>>
>>
>> _______________________________________________
>> 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 Thu Mar 17 2016 - 17:30:03 PDT
