Hi Dave
These pdb files (below) were generated using the leap.in I am sending
you. I removed the water and sections to make them smaller. The problem
of the misplacement of "TER" comes when I have water AND when I have my
three metals present. If I only have two metals the "TER"s are placed
correctly (see TWO.CU.nw.pdb below). The file THREE.CU.nw.pdb (also
below) was made in an identical manner as TWO.CU.nw.pdb except that the
third metal (CUB) was added and this causes the misplacement of "TER".
If there is something else I am forgetting to send you that might make
this clearer please let me know. The last file pasted in email is the
"leap.in" files.
Thanks, Steve
P.S. I tried to send as attachments but my emails would not show up on
the AMBER site.
TWO.CU.nw.pdb File:
..
..
..
ATOM 8554 CZ2 TRP 547 34.083 71.750 42.874
ATOM 8555 HZ2 TRP 547 35.031 72.285 42.938
ATOM 8556 CH2 TRP 547 33.692 70.975 41.771
ATOM 8557 HH2 TRP 547 34.331 70.899 40.891
ATOM 8558 CZ3 TRP 547 32.468 70.284 41.787
ATOM 8559 HZ3 TRP 547 32.153 69.655 40.955
ATOM 8560 CE3 TRP 547 31.610 70.391 42.895
ATOM 8561 HE3 TRP 547 30.674 69.837 42.831
ATOM 8562 CD2 TRP 547 31.953 71.197 44.005
ATOM 8563 C TRP 547 28.785 73.434 45.752
ATOM 8564 O TRP 547 28.642 73.631 46.962
ATOM 8565 OXT TRP 547 28.915 74.309 45.286
TER
ATOM 8566 N LEU 548 49.168 21.498 95.980
ATOM 8567 H1 LEU 548 48.206 21.443 96.283
ATOM 8568 H2 LEU 548 49.660 22.145 96.580
ATOM 8569 H3 LEU 548 49.522 20.561 95.850
ATOM 8570 CA LEU 548 49.192 22.117 94.633
ATOM 8571 HA LEU 548 49.783 23.033 94.656
ATOM 8572 CB LEU 548 49.823 21.149 93.610
ATOM 8573 2HB LEU 548 49.490 20.144 93.868
ATOM 8574 3HB LEU 548 49.443 21.416 92.624
ATOM 8575 CG LEU 548 51.360 21.190 93.594
ATOM 8576 HG LEU 548 51.732 21.156 94.618
ATOM 8577 CD1 LEU 548 51.906 19.987 92.811
ATOM 8578 1HD1 LEU 548 51.535 20.021 91.787
..
..
ATOM 12620 3HD1 LEU 807 52.832 16.331 91.093
ATOM 12621 CD2 LEU 807 56.069 17.451 90.775
ATOM 12622 1HD2 LEU 807 56.655 17.897 89.971
ATOM 12623 2HD2 LEU 807 55.984 18.161 91.598
ATOM 12624 3HD2 LEU 807 56.565 16.546 91.126
ATOM 12625 C LEU 807 52.512 16.616 87.977
ATOM 12626 O LEU 807 52.322 16.676 86.734
ATOM 12627 OXT LEU 807 51.931 17.391 88.772
TER
ATOM 12628 N ALA 808 24.832 58.038 26.958
ATOM 12629 H1 ALA 808 24.274 57.345 26.480
ATOM 12630 H2 ALA 808 24.215 58.680 27.434
ATOM 12631 H3 ALA 808 25.565 57.568 27.470
ATOM 12632 CA ALA 808 25.532 58.855 25.932
ATOM 12633 HA ALA 808 25.215 59.878 26.135
ATOM 12634 CB ALA 808 27.058 58.780 26.067
ATOM 12635 1HB ALA 808 27.393 57.764 25.858
ATOM 12636 2HB ALA 808 27.521 59.467 25.358
ATOM 12637 3HB ALA 808 27.348 59.056 27.081
ATOM 12638 C ALA 808 25.110 58.516 24.496
ATOM 12639 O ALA 808 24.663 57.404 24.224
..
..
ATOM 16820 NE2 GLN 1072 72.247 30.758 37.407
ATOM 16821 1HE2 GLN 1072 71.246 30.835 37.301
ATOM 16822 2HE2 GLN 1072 72.647 30.020 37.969
ATOM 16823 C GLN 1072 74.323 30.303 40.060
ATOM 16824 O GLN 1072 74.755 30.057 41.212
ATOM 16825 OXT GLN 1072 73.892 29.455 39.244
TER
ATOM 16826 CU CUA 1073 48.484 24.911 66.640
TER
ATOM 16827 CU CUA 1074 50.415 23.216 67.258
END
THREE.CU.nw.pdb File (below)
..
..
ATOM 8553 CE2 TRP 547 33.217 71.856 43.971
ATOM 8554 CZ2 TRP 547 34.083 71.750 42.874
ATOM 8555 HZ2 TRP 547 35.031 72.285 42.938
ATOM 8556 CH2 TRP 547 33.692 70.975 41.771
ATOM 8557 HH2 TRP 547 34.331 70.899 40.891
ATOM 8558 CZ3 TRP 547 32.468 70.284 41.787
ATOM 8559 HZ3 TRP 547 32.153 69.655 40.955
ATOM 8560 CE3 TRP 547 31.610 70.391 42.895
ATOM 8561 HE3 TRP 547 30.674 69.837 42.831
ATOM 8562 CD2 TRP 547 31.953 71.197 44.005
ATOM 8563 C TRP 547 28.785 73.434 45.752
ATOM 8564 O TRP 547 28.642 73.631 46.962
ATOM 8565 OXT TRP 547 28.915 74.309 45.286
ATOM 8566 N LEU 548 49.168 21.498 95.980
TER
ATOM 8567 H1 LEU 548 48.206 21.443 96.283
ATOM 8568 H2 LEU 548 49.660 22.145 96.580
ATOM 8569 H3 LEU 548 49.522 20.561 95.850
ATOM 8570 CA LEU 548 49.192 22.117 94.633
ATOM 8571 HA LEU 548 49.783 23.033 94.656
ATOM 8572 CB LEU 548 49.823 21.149 93.610
ATOM 8573 2HB LEU 548 49.490 20.144 93.868
ATOM 8574 3HB LEU 548 49.443 21.416 92.624
ATOM 8575 CG LEU 548 51.360 21.190 93.594
ATOM 8576 HG LEU 548 51.732 21.156 94.618
ATOM 8577 CD1 LEU 548 51.906 19.987 92.811
ATOM 8578 1HD1 LEU 548 51.535 20.021 91.787
ATOM 8579 2HD1 LEU 548 52.996 20.022 92.804
ATOM 8580 3HD1 LEU 548 51.576 19.064 93.286
ATOM 8581 CD2 LEU 548 51.823 22.490 92.928
..
..
ATOM 12621 CD2 LEU 807 56.069 17.451 90.775
ATOM 12622 1HD2 LEU 807 56.655 17.897 89.971
ATOM 12623 2HD2 LEU 807 55.984 18.161 91.598
ATOM 12624 3HD2 LEU 807 56.565 16.546 91.126
ATOM 12625 C LEU 807 52.512 16.616 87.977
ATOM 12626 O LEU 807 52.322 16.676 86.734
ATOM 12627 OXT LEU 807 51.931 17.391 88.772
ATOM 12628 N ALA 808 24.832 58.038 26.958
TER
ATOM 12629 H1 ALA 808 24.274 57.345 26.480
ATOM 12630 H2 ALA 808 24.215 58.680 27.434
ATOM 12631 H3 ALA 808 25.565 57.568 27.470
ATOM 12632 CA ALA 808 25.532 58.855 25.932
ATOM 12633 HA ALA 808 25.215 59.878 26.135
ATOM 12634 CB ALA 808 27.058 58.780 26.067
ATOM 12635 1HB ALA 808 27.393 57.764 25.858
ATOM 12636 2HB ALA 808 27.521 59.467 25.358
ATOM 12637 3HB ALA 808 27.348 59.056 27.081
ATOM 12638 C ALA 808 25.110 58.516 24.496
ATOM 12639 O ALA 808 24.663 57.404 24.224
ATOM 12640 N HIE 809 25.237 59.509 23.607
ATOM 12641 H HIE 809 25.533 60.390 24.004
ATOM 12642 CA HIE 809 24.938 59.459 22.176
ATOM 12643 HA HIE 809 25.134 58.469 21.766
..
..
ATOM 16823 C GLN 1072 74.323 30.303 40.060
ATOM 16824 O GLN 1072 74.755 30.057 41.212
ATOM 16825 OXT GLN 1072 73.892 29.455 39.244
ATOM 16826 CU CUA 1073 48.484 24.911 66.640
TER
ATOM 16827 CU CUA 1074 50.415 23.216 67.258
TER
ATOM 16828 CU CUB 1075 48.175 45.879 60.797
END
Leap.in File
source leaprc.ff03
source leaprc.gaff
loadAmberParams Modfrcmod5.hemall
loadOff HEA.lib
loadOff LIP.lib
loadOff cal.lib
loadOff cua.lib
loadOff cub.lib
#loadOff MG.lib
loadOff HIX.lib
loadOff HIY.lib
loadOff HIZ.lib
CcO=loadPdb THREE.CU.pdb
#addAtomType {{"N5" "NY2" "sp2"}}
bond CcO.288.16 CcO.284.16
bond CcO.421.13 CcO.1090.1
bond CcO.102.13 CcO.1090.1
bond CcO.419.13 CcO.1091.1
bond CcO.333.16 CcO.1088.1
bond CcO.334.16 CcO.1088.1
bond CcO.284.10 CcO.1088.1
deleteBond CcO.333.13 CcO.1088.1
remove CcO CcO.288.17
remove CcO CcO.284.11
deleteBond CcO.64.8 CcO.88.8
set CcO.284 connect0 CcO.284.N
set CcO.284 connect1 CcO.284.C
set CcO.333 connect0 CcO.333.N
set CcO.333 connect1 CcO.333.C
set CcO.334 connect0 CcO.334.N
set CcO.334 connect1 CcO.334
#AddIons CcO Na+ 0
SolvateBox CcO TP3 1
saveamberparm CcO CcOW.prmtop CcOW.inpcrd
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Received on Sun Aug 19 2007 - 06:07:28 PDT
