AMBER Archive (2008)

Subject: Re: AMBER: VMD Movie .mdcrd file ptraj

From: David Watson (
Date: Fri Jun 06 2008 - 09:57:16 CDT

>From what I understand, if you are calling ptraj from the
command line, then you need to specify it as such:

    ptraj mymolecule.prmtop mytrajfile.traj

where: mymolecule.prmtop is whatever your topology file name
is, and mytrajfile.traj is the whatever you have named the
file containing your ptraj script commands.

If you are dumping a new set of MD coordinates, then in VMD
you will first need to create a new molecule, browse for
your >topology< file and load it.

Next you should make sure that the molecule is highlighted,
and then "Load Data into Molecule..."
At this point, browse for your MD coordinate file, and make
sure that it loads as either an "AMBER Coordinates" file, or
"AMBER Coordinates with Periodic Box", depending upon
whether you are using periodic conditions in your

----- Original Message Follows -----
From: "Campbell, Patrick" <>
To: <>
Subject: AMBER: VMD Movie .mdcrd file ptraj
Date: Fri, 6 Jun 2008 09:22:50 -0400

> Hello All,
> I previously mentioned that I was having difficulty
> generating a trajectory movie using my .prmtop and .mdcrd
> files in VMD. It was recommended that checking of the
> .mdcrd file in ptraj was the best follow up step to ensure
> that the file was not corrupted.
> True to these wishes, I followed on the example of
> Tutorial 8 ( Case Study: All Atom Structure Prediction and
> Folding Simulations of a Stable Protein by Ross Walker )
> and got an output file that showed no errors (see
> attachment).
> I would welcome any suggestions as to how I should proceed
> from this point onwards to realize my ambition of
> generating a trajectory movie in VMD.
> Thanks much and have a great day!
> Pat
> [Attachment: extract_705.out]
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)