AMBER Archive (2007)

Subject: AMBER: Missplaced TERs

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Aug 16 2007 - 13:35:26 CDT

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

 

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu