Dear Amber users,
I came across this problem when I tried to auto-image protein kinase A in a
10A solvent box. Looks like some of the atoms could not be recognized and
thus the center of mass of the protein was mis-calculated. Turned out the
protein was not auto-imaged but just flipped 180 degrees. (I was trying to
use auto-image to fix the "protein breaks apart at the edge of solvent box"
problem)
Here's what I get from CPPTRAJ:
CPPTRAJ: Trajectory Analysis. V13.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file cpptraj.in
[parm ../3TNP-with2ADP2MG.prmtop]
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
Warning: Could not determine atomic number from name [DX1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
Warning: Could not determine atomic number from name [DY1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
Warning: Could not determine atomic number from name [DY2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
Warning: Could not determine atomic number from name [DX2 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
Warning: Could not determine atomic number from name [DZ1 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
Warning: Could not determine atomic number from name [DZ2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
Warning: Could not determine atomic number from name [DX1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
Warning: Could not determine atomic number from name [DY1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
Warning: Could not determine atomic number from name [DY2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
Warning: Could not determine atomic number from name [DX2 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
Warning: Could not determine atomic number from name [DZ1 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
Warning: Could not determine atomic number from name [DZ2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
Warning: Could not determine atomic number from name [DX1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
Warning: Could not determine atomic number from name [DY1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
Warning: Could not determine atomic number from name [DY2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
Warning: Could not determine atomic number from name [DX2 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
Warning: Could not determine atomic number from name [DZ1 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
Warning: Could not determine atomic number from name [DZ2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
Warning: Could not determine atomic number from name [DX1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
Warning: Could not determine atomic number from name [DY1 ]
Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
Warning: Could not determine atomic number from name [DY2 ]
Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
Warning: Could not determine atomic number from name [DX2 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
Warning: Could not determine atomic number from name [DZ1 ]
Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
Warning: Could not determine atomic number from name [DZ2 ]
[trajin ../prod113TNP-with2ADP2MG.mdcrd]
[prod113TNP-with2ADP2MG.mdcrd] contains 2500 frames.
[trajin ../prod123TNP-with2ADP2MG.mdcrd]
[prod123TNP-with2ADP2MG.mdcrd] contains 2500 frames.
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first
molecule.
[trajout 3TNP-with2ADP2MG-prod-51-60ns.mdcrd netcdf]
[run]
How do I fix this issue? Any help would be greatly appreciated.
Thanks,
Richard
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Received on Mon Aug 05 2013 - 13:00:03 PDT
