AMBER Archive (2008)

Subject: AMBER: misplacement of TER by leap

From: Jena M (jeninhas_at_hotmail.com)
Date: Mon May 05 2008 - 06:00:55 CDT

Hi,
 
After using leap to build the top and crd files I used ambpdb to obtain the corresponding pdb file. Strangely, leap puts a TER in the wrong place, separating residue 661:
 
 
ATOM 10697 N THR 660 57.725 23.574 52.493
ATOM 10698 H THR 660 57.894 24.352 51.871
ATOM 10699 CA THR 660 57.629 22.230 51.915
ATOM 10700 HA THR 660 58.048 21.493 52.600
ATOM 10701 CB THR 660 56.148 21.834 51.598
ATOM 10702 HB THR 660 56.139 20.843 51.144
ATOM 10703 CG2 THR 660 55.302 21.819 52.876
ATOM 10704 1HG2 THR 660 55.311 22.810 53.329
ATOM 10705 2HG2 THR 660 54.277 21.541 52.630
ATOM 10706 3HG2 THR 660 55.716 21.095 53.578
ATOM 10707 OG1 THR 660 55.586 22.758 50.655
ATOM 10708 1HG THR 660 54.679 22.509 50.465
ATOM 10709 C THR 660 58.450 22.130 50.623
ATOM 10710 O THR 660 59.700 22.093 50.726
ATOM 10711 OXT THR 660 57.890 22.061 49.531
ATOM 10712 N LYS 661 39.901 63.675 56.005
TER
ATOM 10713 H1 LYS 661 40.343 62.832 55.666
ATOM 10714 H2 LYS 661 40.505 64.460 55.807
ATOM 10715 H3 LYS 661 38.941 63.686 55.693
ATOM 10716 CA LYS 661 39.833 63.598 57.459
ATOM 10717 HA LYS 661 40.380 64.433 57.897
ATOM 10718 CB LYS 661 38.368 63.662 57.940
ATOM 10719 2HB LYS 661 38.410 63.645 59.029
ATOM 10720 3HB LYS 661 37.986 64.627 57.606
ATOM 10721 CG LYS 661 37.440 62.549 57.449
ATOM 10722 2HG LYS 661 37.445 62.544 56.359
ATOM 10723 3HG LYS 661 37.813 61.593 57.818
ATOM 10724 CD LYS 661 36.009 62.768 57.952
ATOM 10725 2HD LYS 661 35.671 63.743 57.602
ATOM 10726 3HD LYS 661 35.376 61.990 57.526
ATOM 10727 CE LYS 661 35.923 62.716 59.476
ATOM 10728 2HE LYS 661 36.212 61.715 59.795
ATOM 10729 3HE LYS 661 36.630 63.443 59.877
ATOM 10730 NZ LYS 661 34.551 63.023 59.983
ATOM 10731 1HZ LYS 661 33.897 62.350 59.611
ATOM 10732 2HZ LYS 661 34.547 62.976 60.992
ATOM 10733 3HZ LYS 661 34.283 63.951 59.688
ATOM 10734 C LYS 661 40.520 62.347 58.014
ATOM 10735 O LYS 661 39.995 61.684 58.910
 
I made some tests and I think the problem is with the command “solvatebox prot TIP3PBOX 18.0”, because if I save the top and crd files in vacuum this problem with residue 661 does not happen. Does anyone know what might be causing this and how to solve? I am using amber8.
 
Thanks,
Jena
 
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