VMD-L Mailing List

From: Diego Vazquez (dsvazquez86_at_gmail.com)
Date: Fri Oct 30 2015 - 07:21:19 CDT

If your trajectory is in .nc there should be no problem with that, vmd
recognize automatically the binary file...unless you have a problem with
the topology file (e.g. the atom number don´t match!!)
On Oct 30, 2015 8:17 AM, "Atila Petrosian" <atila.petrosian_at_gmail.com>
wrote:

> Dear Diego,
>
> Thanks for your answer.
>
> I converted .mdcrd file to .nc file. In VMD, there is amber7 parm in file
> type section of molecule file browser window. But there is no netcdf in
> file type section.
>
> After loading .prmtop as AMBER7 parm, how to load .nc file as netcdf? I
> load .nc file, but nothing happened.
>
> I have a general question. Is there all things needed for analysis of
> trajectory in .nc file?
>
> After converting .mdcrd files to .nc files, can I deleted .mdcrd files?
> There is no enough memory in my computer system.
>
> Best,
> Atila
>
> On Fri, Oct 30, 2015 at 12:32 PM, Diego Vazquez <dsvazquez86_at_gmail.com>
> wrote:
>
>> Dear Atila,
>>
>> Just load your .prmtop as AMBER7 parm and the .nc file into the prmtop as
>> NetCDF...that's all!
>>
>> On 30 October 2015 at 04:22, Atila Petrosian <atila.petrosian_at_gmail.com>
>> wrote:
>>
>>> Dear vmd users,
>>>
>>> I saw my amber trajectories by loading *.prmtop and *.mdcrd fils.
>>>
>>> Now, I have *.netcdf file instead of *.mdcrd file.
>>>
>>> In this case, how to see my new trajectory using vmd?
>>>
>>> Best,
>>> Atila
>>>
>>
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>>
>>
>> **************************************************
>> Lic. Diego Sebastian Vazquez
>> Laboratorio de Biofísica de Proteínas
>> IQUIFIB - Departamento de Química Biológica
>> Facultad de Farmacia y Bioquímica
>> Universidad de Buenos Aires, Argentina
>> Junín 956 (1113)
>> Tel: 1534476306
>> dsv_at_qb.ffyb.uba.ar
>>
>
>