On Tue, Jul 1, 2014 at 8:33 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> trajin filename.mdcrd
> trajout filename.pdb pdb
>
> Then run
>
> $AMBERHOME/bin/cpptraj -p prmtop < textfile
>
FYI in addition to this, with recent versions of cpptraj you can also
convert trajectories in one step from the command line (cpptraj will
determine the desired output format from the extension):
$AMBERHOME/bin/cpptraj -p prmtop -y filename.mdcrd -x filename.pdb
-Dan
>
> 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
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 02 2014 - 07:30:06 PDT
