[gmx-users] Problem with reading AMBER trajectories

Sat Oct 26 09:20:08 CEST 2013

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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>
>