Re: [gmx-users] How to read in netcdf with GROMACS?‏

[Bala subramanian]

Hi,
Read the error information carefully. Probably you are trying to read a
amber trajectory. Try installing vmd and set the VMD_PLUGIN_PATH variable
to the plugin directory inside vmd installation. Gromacs can then read the
trajectory using the vmd plugin.

On Sat, May 26, 2012 at 6:42 PM, a a <patd_2 at hotmail.com> wrote:

>  Dear Sir/Madam,
>
> I am trying to do the following analysis with GROMACS:
>
> /usr/local/gromacs/bin/g_covar -s my.pdb -f my.netcdf -o -v
>
> However, I found the following error message:
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> GROMACS will now assume it to be a trajectory and will try to open it
> using the VMD plug-ins.
> This will only work in case the VMD plugins are found and it is a
> trajectory format supported by VMD.
>
> VMD_PLUGIN_PATH not set. Using default location:
> /usr/local/lib/vmd/plugins/*/molfile
>
> Could not open any VMD library.
> Last error:
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xyzplugin.so: wrong ELF
> class: ELFCLASS64
>
> -------------------------------------------------------
> Program g_covar, VERSION 4.5.5
> Source code file: trxio.c, line: 870
>
> Fatal error:
> Not supported in read_first_frame: D1_md7to23.netcdf
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> However, when I double check my
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile directory, I can see
> netcdfplugin.so file.
>
> Why the file cannot recognize to use netcdfplugin.so file to read
> my.netcdf file, but instead trying to use the xyzplugin.so file?
>
> I have also set the following path in .bashrc file already.
> VMD_PLUGIN_PATH=/mydirectory/vmd/lib/vmd/plugins/LINUX/**molfile
>
> Did I do anything wrong?
>
> Best regards,
>
> Catherine
>
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-- 
C. Balasubramanian
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