Also FYI the nastruct command in cpptraj uses 3dna algorithms under the
hood, so you may want to give that a try.
-Dan
On Thursday, March 17, 2016, Daniel Roe <daniel.r.roe.gmail.com> 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
> <javascript:_e(%7B%7D,'cvml','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>
>> 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
>>
>
>
> --
> -------------------------
> 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)
>
--
-------------------------
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 Thu Mar 17 2016 - 17:30:05 PDT
