Hello,
I compiled amber8 which Intel Fortran 8.0 and Intel(R) Math Kernel
Library v7.0 on linux RedHat 9.0. I made some time ago a small tetrapeptide to
teach computer students how to measure torsion angles in proteins with the
following input file.
................................................................................
moltor = sequence { NALA ALA ALA CALA }
impose moltor { 1 2 } { { N CA C N 0.0 } { CA C N CA 60.0 } { C N CA C 120.0 } }
impose moltor { 2 3 } { { N CA C N 180.0 } { CA C N CA -120.0 } { C N CA C -60.0 } }
impose moltor { 3 4 } { { N CA C N 180.0 } { CA C N CA -90.0 } { C N CA C 90.0 } }
measuregeom moltor.1.N moltor.1.CA moltor.1.C moltor.2.N
measuregeom moltor.1.CA moltor.1.C moltor.2.N moltor.2.CA
measuregeom moltor.1.C moltor.2.N moltor.2.CA moltor.2.C
measuregeom moltor.2.N moltor.2.CA moltor.2.C moltor.3.N
measuregeom moltor.2.CA moltor.2.C moltor.3.N moltor.3.CA
measuregeom moltor.2.C moltor.3.N moltor.3.CA moltor.3.C
measuregeom moltor.3.N moltor.3.CA moltor.3.C moltor.4.N
measuregeom moltor.3.CA moltor.3.C moltor.4.N moltor.4.CA
measuregeom moltor.3.C moltor.4.N moltor.4.CA moltor.4.C
savepdb moltor moltorbor.pdb
quit
................................................................................
With amber 6.0 on alpha it gave the values I impose, but with amber8 on linux
the two first are wrong, here the values for the 9 angles.
Torsion angle: -13.20 degrees
Torsion angle: 73.55 degrees
Torsion angle: 120.00 degrees
Torsion angle: -180.00 degrees
Torsion angle: -120.00 degrees
Torsion angle: -60.00 degrees
Torsion angle: -180.00 degrees
Torsion angle: -90.00 degrees
Torsion angle: 90.00 degrees
It surprised me that the two first values are no correct on linux while
the same input file with amber 8.0 on alpha again, gave the right values.
Any ideas? Maybe it is not important, I am just trying to understand
the differences and why the computer students find values that are not in my
input file.
Have fun
Guillermo Mulliert
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Received on Tue Apr 05 2005 - 08:53:00 PDT
