[gmx-users] Problem with reading AMBER trajectories

Mark Abraham mark.j.abraham at gmail.com
Fri Oct 18 14:51:14 CEST 2013


OK. All GROMACS does is feed your filename extension to the VMD library and
let it choose how to read the file based on that. If that doesn't make
sense (and it seems it doesn't, because GROMACS wasn't told about the
number of atoms, and it needs to know), then the ball is back to you to
choose the filename extension in the way the plugin needs. I suggest you
check out http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ and try some
alternatives.

Mark


On Fri, Oct 18, 2013 at 2:10 PM, anu chandra <anu80125 at gmail.com> wrote:

> Hi Mark,
>
> Yes. I do can able to load the trajectories successfully in VMD with the
> file format option of ' AMBER coordinate with periodic box'. I am using VMD
> 1.9 version.
>
> Regards
> Anu
>
>
>
>
> On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > 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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