Hi, FYI, when I feed the coordinates in '.binpos' format, which I generated after loading the same '.crd' file to VMD, could able to do the job. What I infer from this is that the VMD molfile, for reading AMBER '.crd' trajectories, has made for reading AMBER 7 '.crd' formatted trajectories which can not able to read latest ones.
On Sat, Oct 26, 2013 at 12:21 PM, anu chandra <anu80...@gmail.com> wrote: > 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
