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
>
--
-------------------------
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 Thu Mar 17 2016 - 17:30:04 PDT
