[gmx-users] Problem with reading AMBER trajectories

[anu chandra]

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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