Are there any papers or data available on the results of the latest
Amber parameters for simple peptides?
Below, I have attached the PDB files for two conformations of Alanine
Tetrapeptide from
the frequently cited Beechy et al paper in JACS 1997-119. In the
following experiment,
I minimized the potential energy of these two conformations using the
parm99.dat parameters + 2002 charges (all_amino02.in). As a result of
energy minimization, both conformations converge to a single
conformation. In earlier Amber parameter sets, such as ff94, these two
conformations remain distinct, when minimized.
I appreciate any comments confirming or refuting this result and/or any
additional references.
Regards
Sia Meshkat
----------------------------- Conformation 4 PDB file
-------------------------
HEADER ALANINE TETRAPEPTIDE CONFORMATION 4
COMPND
SOURCE
ATOM 1 CH3 ACE A 1 0.000 -0.000 0.000 0.00 0.00
ATOM 2 C ACE A 1 0.000 -0.000 1.510 0.00 0.00
ATOM 3 O ACE A 1 0.000 -1.029 2.166 0.00 0.00
ATOM 4 1H ACE A 1 -0.747 0.747 -0.341 0.00 0.00
ATOM 5 2H ACE A 1 -0.307 -1.011 -0.341 0.00 0.00
ATOM 6 3H ACE A 1 1.011 0.307 -0.341 0.00 0.00
ATOM 7 N ALA A 2 0.000 1.236 2.027 0.00 0.00
ATOM 8 CA ALA A 2 0.000 1.447 3.472 0.00 0.00
ATOM 9 C ALA A 2 -0.551 2.805 3.835 0.00 0.00
ATOM 10 O ALA A 2 -0.627 3.718 3.030 0.00 0.00
ATOM 11 H ALA A 2 0.000 2.026 1.381 0.00 0.00
ATOM 12 HA ALA A 2 -0.637 0.679 3.958 0.00 0.00
ATOM 13 CB ALA A 2 1.443 1.367 4.003 0.00 0.00
ATOM 14 1HB ALA A 2 1.441 1.527 5.101 0.00 0.00
ATOM 15 2HB ALA A 2 2.059 2.152 3.517 0.00 0.00
ATOM 16 3HB ALA A 2 1.864 0.365 3.778 0.00 0.00
ATOM 17 N ALA A 3 -0.935 2.881 5.117 0.00 0.00
ATOM 18 CA ALA A 3 -1.495 4.114 5.662 0.00 0.00
ATOM 19 C ALA A 3 -0.418 5.022 6.204 0.00 0.00
ATOM 20 O ALA A 3 -0.117 5.050 7.386 0.00 0.00
ATOM 21 H ALA A 3 -0.824 2.052 5.700 0.00 0.00
ATOM 22 HA ALA A 3 -2.033 4.663 4.861 0.00 0.00
ATOM 23 CB ALA A 3 -2.452 3.776 6.820 0.00 0.00
ATOM 24 1HB ALA A 3 -2.877 4.714 7.233 0.00 0.00
ATOM 25 2HB ALA A 3 -1.893 3.242 7.617 0.00 0.00
ATOM 26 3HB ALA A 3 -3.275 3.133 6.443 0.00 0.00
ATOM 27 N ALA A 4 0.153 5.774 5.252 0.00 0.00
ATOM 28 CA ALA A 4 1.218 6.718 5.577 0.00 0.00
ATOM 29 C ALA A 4 1.309 7.826 4.556 0.00 0.00
ATOM 30 O ALA A 4 0.956 7.680 3.397 0.00 0.00
ATOM 31 H ALA A 4 -0.180 5.666 4.294 0.00 0.00
ATOM 32 HA ALA A 4 1.015 7.180 6.565 0.00 0.00
ATOM 33 CB ALA A 4 2.570 5.981 5.594 0.00 0.00
ATOM 34 1HB ALA A 4 3.379 6.700 5.841 0.00 0.00
ATOM 35 2HB ALA A 4 2.762 5.540 4.594 0.00 0.00
ATOM 36 3HB ALA A 4 2.543 5.179 6.361 0.00 0.00
ATOM 37 N NME A 5 1.812 8.959 5.065 0.00 0.00
ATOM 38 CH3 NME A 5 1.979 10.148 4.234 0.00 0.00
ATOM 39 H NME A 5 2.074 8.966 6.051 0.00 0.00
ATOM 40 1H NME A 5 2.977 10.595 4.425 0.00 0.00
ATOM 41 2H NME A 5 1.189 10.887 4.481 0.00 0.00
ATOM 42 3H NME A 5 1.897 9.866 3.164 0.00 0.00
END
------------------------------------------------------------------------
-------
----------------------------- Conformation 5 PDB file
-------------------------
HEADER ALANINE TETRAPEPTIDE CONFORMATION 5
COMPND
SOURCE
ATOM 1 CH3 ACE A 1 0.000 -0.000 -0.000 0.00 0.00
ATOM 2 C ACE A 1 0.000 -0.000 1.510 0.00 0.00
ATOM 3 O ACE A 1 -0.000 -1.029 2.166 0.00 0.00
ATOM 4 1H ACE A 1 -0.747 0.747 -0.341 0.00 0.00
ATOM 5 2H ACE A 1 -0.307 -1.011 -0.341 0.00 0.00
ATOM 6 3H ACE A 1 1.011 0.307 -0.341 0.00 0.00
ATOM 7 N ALA A 2 0.000 1.236 2.027 0.00 0.00
ATOM 8 CA ALA A 2 0.000 1.447 3.472 0.00 0.00
ATOM 9 C ALA A 2 -0.544 2.808 3.835 0.00 0.00
ATOM 10 O ALA A 2 -0.760 3.671 3.001 0.00 0.00
ATOM 11 H ALA A 2 0.000 2.026 1.381 0.00 0.00
ATOM 12 HA ALA A 2 -0.641 0.682 3.958 0.00 0.00
ATOM 13 CB ALA A 2 1.442 1.359 4.004 0.00 0.00
ATOM 14 1HB ALA A 2 1.440 1.520 5.102 0.00 0.00
ATOM 15 2HB ALA A 2 2.063 2.141 3.518 0.00 0.00
ATOM 16 3HB ALA A 2 1.858 0.355 3.779 0.00 0.00
ATOM 17 N ALA A 3 -0.755 2.946 5.151 0.00 0.00
ATOM 18 CA ALA A 3 -1.279 4.192 5.702 0.00 0.00
ATOM 19 C ALA A 3 -0.218 5.266 5.758 0.00 0.00
ATOM 20 O ALA A 3 -0.490 6.452 5.844 0.00 0.00
ATOM 21 H ALA A 3 -0.537 2.155 5.757 0.00 0.00
ATOM 22 HA ALA A 3 -2.105 4.563 5.059 0.00 0.00
ATOM 23 CB ALA A 3 -1.780 3.950 7.138 0.00 0.00
ATOM 24 1HB ALA A 3 -2.178 4.898 7.555 0.00 0.00
ATOM 25 2HB ALA A 3 -0.936 3.596 7.767 0.00 0.00
ATOM 26 3HB ALA A 3 -2.585 3.186 7.123 0.00 0.00
ATOM 27 N ALA A 4 1.024 4.767 5.703 0.00 0.00
ATOM 28 CA ALA A 4 2.189 5.646 5.744 0.00 0.00
ATOM 29 C ALA A 4 3.382 5.022 5.060 0.00 0.00
ATOM 30 O ALA A 4 3.464 3.822 4.853 0.00 0.00
ATOM 31 H ALA A 4 1.132 3.756 5.632 0.00 0.00
ATOM 32 HA ALA A 4 1.955 6.597 5.221 0.00 0.00
ATOM 33 CB ALA A 4 2.576 5.919 7.210 0.00 0.00
ATOM 34 1HB ALA A 4 3.462 6.587 7.239 0.00 0.00
ATOM 35 2HB ALA A 4 2.822 4.959 7.711 0.00 0.00
ATOM 36 3HB ALA A 4 1.727 6.409 7.731 0.00 0.00
ATOM 37 N NME A 5 4.313 5.923 4.719 0.00 0.00
ATOM 38 CH3 NME A 5 5.543 5.515 4.046 0.00 0.00
ATOM 39 H NME A 5 4.136 6.902 4.943 0.00 0.00
ATOM 40 1H NME A 5 6.409 6.025 4.516 0.00 0.00
ATOM 41 2H NME A 5 5.487 5.792 2.973 0.00 0.00
ATOM 42 3H NME A 5 5.667 4.415 4.135 0.00 0.00
END
------------------------------------------------------------------------
-------
Received on Mon Jul 07 2003 - 17:53:00 PDT
