[AMBER] ptraj problems

From: Christoph Malisi <christoph.malisi.tuebingen.mpg.de>
Date: Thu, 24 Mar 2011 15:05:42 +0100


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 MMPBSA.py (my actual goal), I also
have problems when using frames larger than ~5000. I figure since
MMPBSA.py 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,

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Received on Thu Mar 24 2011 - 07:30:03 PDT
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