[gmx-users] Problem with reading AMBER trajectories

[Mark Abraham]

Can this file be opened in VMD itself?

Mark
On Oct 18, 2013 6:21 AM, "anu chandra" <anu80125 at gmail.com> wrote:

> Dear Gromacs users,
>
> I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few
> analysis. Unfortunately I ended-up with the following error.
>
> ############################################################
> 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.
>
> Using VMD plugin: crd (AMBER Coordinates)
>
> Format of file md.crd does not record number of atoms.
>
> -------------------------------------------------------
> Program g_covar, VERSION 4.6.1
> Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035
>
> Fatal error:
> Not supported in read_first_frame: md.crd
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> ############################################################
>
>
>
> While browsing through the GROMACS mail-list, I came to know that it might
> be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake
> using the following command
>
> ############################################################
> CMAKE_PREFIX_PATH=/usr/include/libltdl cmake
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc
> -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a
> -DFFTWF_INCLUDE_DIR=/usr/lib/ ../
> ############################################################
>
> But, the same problem came-up again. Can anyone help me to figure out what
> went wrong with my Gromacs installation?
>
> Many thanks in advance.
>
> Regards
> Anu
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