Dear Prof. Case
Thanks for the reply.
On Sat, Oct 26, 2013 at 6:28 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Oct 26, 2013, anu chandra wrote:
> >
> > I am trying to use the Amber crd trajectories in Gromacs. Here, Gromcas
> use
> > the VMD molfile pulgin for reading the crd files. From the plugin
> details,
> > I came to know that the pulgin reads .crd files with AMBER7 format and I
> > could not able to use the plugin for reading the .crd files ( generated
> > with AMBER 12) in Gromcas. As a trial run, when I convert the .crd file
> to
> > .binpos file in VMD, Gromcas successfully read the file with the help of
> > respective plugin in VMD. I wonder is there any difference between the
> .crd
> > file format in AMBER-7 and AMBER-12?
>
> In VMD-lingo, "Amber7" refers to "Amber 7 and all subsequent versions". So
> there should be no difference between Amber7 and Amber12.
>
> One possible problem is that people sometimes mean different things by the
> term ".crd file". Amber doesn't enforce any particular file extensions.
> "coordinates" might mean those in a restart file or in a trajectory file.
> Your use of "binpos" suggests that you might have coordinates in a
> trajectory
> file, but I'm just guessing.
Yes. The .crd file have coordinates from a simulation trajectory.
> What do the top few lines of your .crd file
> look like?
>
The top of the file looks like as follows.
*********************************************************************************************
default_name
33.200 29.437 78.205 32.490 28.791 78.519 32.774 30.194 77.690
33.776
29.742 78.976 34.018 28.738 77.203 34.848 29.380 76.906 34.417
27.800
77.588 33.181 28.443 75.954 31.965 28.608 76.031 33.856 28.005
74.859
34.858 27.936 74.961 33.218 27.429 73.642 32.362 28.071 73.432
34.141
**********************************************************************************************
>
> ....dac
>
Thanks and Regards,
Anu
>
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Received on Sun Oct 27 2013 - 22:00:03 PDT
