VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 30 2015 - 08:28:50 CDT

On Fri, Oct 30, 2015 at 8:46 AM, Atila Petrosian <atila.petrosian_at_gmail.com>
wrote:

> I could see prmtop and mdcrd files using vmd without any problem.
>
> I there was a problem with the topology file, I could not see prmtop and
> mdcrd files.
>

​these two statements seem to contradict each other. surely, wanted to
express something else. please try to reformulate or describe in more
detail.​

>
> Is this problem related to VMD?
>

​what platform (CPU, OS, VMD version) are you running​ on. some file
formats are not supported on all platforms, since the plugins require
external libraries that may not always be available or are not easily
ported. also, there is the occasional change (improvement) between
different versions of VMD.

axel.

​p.s.: i would strongly suggest to not delete original files until your
project is done. disk storage is extremely cheap these days, just get some
large external USB hard drive and make a copy (for archival purposes, and
in addition to your regular backups).
​

>
> On Fri, Oct 30, 2015 at 3:51 PM, Diego Vazquez <dsvazquez86_at_gmail.com>
> wrote:
>
>> 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
>>>>
>>>
>>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.