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

[Rafael I. Silverman y de la Vega]

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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