Re: [AMBER] ptraj problems

From: Jason Swails <>
Date: Thu, 24 Mar 2011 08:35:14 -0700

At one point ptraj had quite some issues with large file sizes. Dan Roe has
since fixed these issues. See recent bug fixes and make sure you apply all
of them. Of specific interest is bugfix.16 of AmberTools 1.4 (this fixes
the exact issue you're describing here).

Future advice (I know that you didn't create this file) is to use NetCDF
trajectories. You can add "netcdf" to the trajout statement to do this.

Hope this helps,

On Thu, Mar 24, 2011 at 7:05 AM, Christoph Malisi <> wrote:

> Hello,
> A coworker (who is not in our lab any more, unfortunately), has left us
> with a amber trajectory of a protein ligand system we are interested in
> (prmtop and mdcrd files). As I understand it, this trajectory was
> created by combining mdcrd files (minimization, heating, equilibration,
> production) with ptraj. The simulation was done with explicit water and
> a periodic boundary box. There are 15000 frames in the trajectory, it is
> around 13 GB in size.
> When playing around with the trajectory, I get strange results:
> * when loading the trajectory in vmd, it seems fine (judging from the
> displayed structures)
> * when trying to produce a movie using Chimera, the structures look
> really wharped
> * when doing a RMSD analysis with ptraj using the commands (protein and
> ligand are residues 1-204)
> trajin trpR.mdcrd
> rms first out trpR.rms :1-204
> the plot looks fine in the first 4954 frames (rms around 2 to 3), the in
> apruptly jumps to just above 18 and stays there with very little
> variability (<0.02), at 9908 it makes another jump to around 18.8, and
> stays there with a little more variability.
> * when writing out a part of the trajectory with ptraj
> trajin trpR.mdcrd 5000 6000
> trajout trpR_5000_6000.mdcrd
> the structures in vmd look very strange, the atoms seem to be contracted
> to a cube-like structure. The coordinates seem all to be in the range
> between 0.0 and 1.0. Same is true when doing PDB snapshots:
> trajin trpR.mdcrd 1 15000 100
> strip :WAT
> strip :Na+
> strip :Cl-
> trajout trpR-Ltrp.pdb pdb
> * When I use this trajectory with (my actual goal), I also
> have problems when using frames larger than ~5000. I figure since
> also uses ptraj that the problem comes from there.
> Does anybody have any idea what is happening here?
> Do I miss some ptraj parameter or argument?
> All this was done with Amber11.
> If you need any files/ data, I'd be happy to provide them.
> Thanks in advance,
> Chris
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Mar 24 2011 - 09:00:04 PDT
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