Re: [AMBER] Understand the AMBER coordinate files

From: Ross Walker <>
Date: Tue, 01 Jul 2014 19:33:36 -0700

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

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

On 7/1/14, 6:52 PM, "Wujie Wang" <> 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
> 52.050 -57.729 48.235 51.689 -56.333 47.259 51.598 -58.283 46.933
> -58.191 47.667 51.224 -59.596 46.455 50.684 -60.150 45.907 51.511
>I guess each consecutive three numbers form a coordinate triplet (xyz),
>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
>AMBER mailing list

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Received on Tue Jul 01 2014 - 20:00:02 PDT
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