[gmx-users] problem with chimera opening gromacs 4.6.5 trajectories

[Mark Abraham]

.tpr file format is basically certain to change with every major or minor
(not patch) release. So you should ask the chimera people to consider
supporting the 5.0 format also - it's unlikely to change further before the
official release.

Mark


On Wed, Apr 23, 2014 at 11:34 PM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:

> Someone already contacted chimera developers about this. Todays daily build
> of chimera opens the files fine.
>
>
> On Wed, Apr 23, 2014 at 1:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/23/14, 4:40 PM, Rafael I. Silverman y de la Vega wrote:
> >
> >> chimera 1.8 crashed. 1.9 (released today) crashed. 1.8.1 crashed. 1.8.1
> >> and
> >> 1.8 both read older trr files just fine, I didnt try 1.9 on an older trr
> >> file.
> >> Maybe its the .tpr file causing the error?
> >>
> >>
> > I think that's the most likely culprit.  The .tpr format has changed due
> > to new features; the Chimera devs will have to update their plugin to
> > interpret the contents properly.
> >
> > -Justin
> >
> >
> >
> >> On Wed, Apr 23, 2014 at 11:20 AM, Rafael I. Silverman y de la Vega <
> >> rsilverm at ucsc.edu> wrote:
> >>
> >>  I'll try 1.8, I've been trying 1.8.1
> >>>
> >>>
> >>> On Wed, Apr 23, 2014 at 11:09 AM, Nicolas Cheron <
> >>> nicolas.cheron.boulot at gmail.com> wrote:
> >>>
> >>>  Which Chimera version are you using? Have you tried the latest (at
> least
> >>>> 1.8)?
> >>>>
> >>>> http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.8.html : "support
> >>>> added for Gromacs 4.6 trajectories"
> >>>>
> >>>> Nicolas
> >>>>
> >>>>
> >>>> 2014-04-23 14:02 GMT-04:00 Rafael I. Silverman y de la Vega <
> >>>> rsilverm at ucsc.edu>:
> >>>>
> >>>>> Hi all
> >>>>> I have been having problems getting chimera to open 4.6 trajectories.
> >>>>> It
> >>>>> opens trajectory files from gromacs 4.5 just fine. (well, at least
> some
> >>>>> chimera builds open the trajecotries).
> >>>>> I tried using gromacs 4.5 trjconv to make xtc readable by chimera,
> but,
> >>>>>
> >>>> of
> >>>>
> >>>>> course that didnt work on the trr made by 4.6.
> >>>>> Will gromacs 5.0 make chimera readable files, or should I go bother
> the
> >>>>> chimera developers?
> >>>>> --
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> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
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