VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Fri Oct 30 2015 - 09:35:26 CDT

Atila,
Axel has explained all. You cannot open nc file under the windows vmd. I do not think that You have any problem with your prmtop or mdcrd file.
As I mentioned open former mdcrd along with corresponding prmtop file under the windows and see if there is any prob.
Zoran
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.