[gmx-users] Problem with reading AMBER trajectories

[anu chandra]

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
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>