VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Fri Oct 30 2015 - 08:17:45 CDT

Hello Atila and Diego,
I think that NetCDF works under linux version of vmd but not under windows. This was the case when I tried to open cdf trajectory. You should reconvert cdf into mdcrd and than open it in windows vmd.
Cheers
Zoran
From: Diego Vazquez
Sent: Friday, October 30, 2015 1:21 PM
To: Atila Petrosian
Cc: VMD
Subject: Re: vmd-l: netcdf trajectory file

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