[gmx-users] Problem with reading AMBER trajectories

Mark Abraham mark.j.abraham at gmail.com
Sat Oct 26 12:59:54 CEST 2013 

Hi,

Seems plausible, and it's good to know you have the plugins working for at
least one format! The question of whether the plugins are out of step with
the main VMD distribution would be best raised on the VMD mailing list (but
search first!). If you do, you might also suggest that the links in the
plugin docs be updated to http://ambermd.org/formats.html

Cheers,

Mark
On Oct 26, 2013 9:20 AM, "anu chandra" <anu80125 at gmail.com> wrote:

> 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 <anu80125 at 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.abraham at 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 <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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