[gmx-users] conversion of desmond trajectory files into gromacs

[Roland Schulz]

On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Really? This is really great!
> Is there any need to specify the location of the vmd libraries?
>
By default it tries to find them at
 /usr/local/lib/vmd/plugins/*/molfile

If you have them installed somewhere else you can specify it by setting
the VMD_PLUGIN_PATH environment variable.

If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this
> somehow still possible?
>
It would be pretty simple to add, that one can read this molecule
information also from pdb or from psf. But I didn't have time to do it. In
case you are interested to do that, I can give you help doing it.

Until someone implements it, one still needs the tpr file. For cases where
it is difficult to generate a top file we have a version of psfgen which
generates a top file from a psf. But we don't have solved the license issue
so far (NAMD license) and thus can't provide this version yet.

Roland


>
> On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote:
>
> In case you use the GIT version of the analysis tools you don't need to
> convert the trajectories first.
> I've added that the analysis tools can read all vmd supported file formats
> if GROMACS finds the vmd libraries.
>
> Roland
>
> On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole <x.periole at rug.nl> wrote:
>
>>
>> Well I guess you want to use gmx analysis tools so you'll have to
>> build the gmx topology of your system when necessary! Often
>> only a pdb file or a gro file is sufficient.
>>
>>
>> On Apr 16, 2010, at 5:24 PM, ram bio wrote:
>>
>>  Thanks Xavier,
>>>
>>> Could you make it more eloborate...
>>>
>>> Ram
>>>
>>> On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole <x.periole at rug.nl>
>>> wrote:
>>>
>>>>
>>>> VMD reads Desmond trajectories and writes GMX format ...
>>>> Rests the topology to deal with ...
>>>>
>>>> On Apr 16, 2010, at 4:15 PM, ram bio wrote:
>>>>
>>>>  Dear All,
>>>>>
>>>>> I have run a dynamics of protein ligand complex in lipid bilayer dppc
>>>>> using desmond software and would like to convert the trajectory files
>>>>> files into gromacs format, is it possible?? if so, please let me know
>>>>> your suggestions.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Ram
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>
>
>
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