Hi, Sorry for the late reply. I have tried all the possibilities with filename extension as mentioned in the VMD molfile details. As said, VMD uses .crd or .crdbox filename extensions for reading Amber trajectories. I have tried with both the options ( ie. with .crd and .crdbox extensions) , but unfortunately both the attempt got failed with same error as shown below
************************************************************************* Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. Calculating the average structure ... The file format of eqc.crdbox is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory! 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: crdbox (AMBER Coordinates with Periodic Box) Format of file eqc.crdbox 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: md1.crdbox For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Hang On to Your Ego" (F. Black) ************************************************************************************************************ Can anyone please help me to figure out what is going wrong here? Many thanks Anu On Fri, Oct 18, 2013 at 6:21 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > -- 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