Thank you!
On Tue, Jul 1, 2014 at 10:33 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Wujie,
>
> The trajectory file in AMBER, in ASCII format, is simply X1, Y1, Z1 -> XN,
> YN, ZN followed by 3 numbers for the box size. It then repeats for the
> next frame with no line break. See
> http://ambermd.org/formats.html#trajectory
>
> Note, it's not really designed to be human readable and requires a
> matching prmtop file. You have several options in terms of your analysis.
> You can use the cpptraj tool that ships with AMBER - this can likely carry
> out all the analysis you want to do. However, if you are more familiar
> with Lammps you may just want to convert the trajectory file into a
> different format and use that to do the analysis with Lammps or whatever
> program you are used to. Cpptraj can do this for you. For example if you
> wanted to convert the trajectory file to a multi-molecule pdb file you
> would create a text file for cpptraj as follows
>
> trajin filename.mdcrd
> trajout filename.pdb pdb
>
> Then run
>
> $AMBERHOME/bin/cpptraj -p prmtop < textfile
>
> I hope that helps.
>
> All the best
> Ross
>
>
>
> On 7/1/14, 6:52 PM, "Wujie Wang" <wwang02.wesleyan.edu> wrote:
>
> >Dear fellow AMBER users
> >
> >I am new to AMBER MD, but have had experiences using LAMMPS. I need to
> >simulate something by AMBER to finish a part of my project.
> >
> >I need to analyze the some data from the trajectory file (.mdcrd) which is
> >straightforward in LAMMPS. However, I do not know what atoms these numbers
> >refer to.
> >
> >49.922 50.127 -56.945 49.053 50.131 -57.352 48.477 51.453 -57.370
> >49.315
> >
> > 52.050 -57.729 48.235 51.689 -56.333 47.259 51.598 -58.283 46.933
> >52.634
> >
> > -58.191 47.667 51.224 -59.596 46.455 50.684 -60.150 45.907 51.511
> >-60.600
> >
> >............................................
> >
> >
> >I guess each consecutive three numbers form a coordinate triplet (xyz),
> >but
> >they are the coordinate of which atom is the question. Should I go to
> >.prmtop to figure out which one is which and how?
> >
> >
> >Thank you
> >
> >
> >Wujie
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jul 02 2014 - 07:00:03 PDT
