From: Atila Petrosian (atila.petrosian_at_gmail.com)
Date: Fri Oct 30 2015 - 08:42:20 CDT

Dear all,

I am using vmd 1.9.1 on windows.

On Fri, Oct 30, 2015 at 4:58 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> 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.
>