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 <anu80...@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.abra...@gmail.com > >wrote: > > > Can this file be opened in VMD itself? > > > > Mark > > On Oct 18, 2013 6:21 AM, "anu chandra" <anu80...@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@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-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
