I use ambpdb to convert a restrt file to a pdb file. If you look at the
pdb file I get, it is kind of strange because ambpdb put TER inside
MET159. It's supposed to be between GLU158 and MET159. The protein is a
dimer, 158 residues for each monomer. Then I checked the structure, the
rmsd between MD trajectory and crystal structure is fine, about 1 ang.
Is it a bug or something?
...........
ATOM 2406 N GLU 158 36.434 53.530 17.579
ATOM 2407 H GLU 158 35.540 53.140 17.843
ATOM 2408 CA GLU 158 36.697 53.794 16.144
ATOM 2409 HA GLU 158 37.390 53.038 15.774
ATOM 2410 CB GLU 158 35.446 53.739 15.324
ATOM 2411 2HB GLU 158 34.712 54.507 15.570
ATOM 2412 3HB GLU 158 35.742 54.035 14.318
ATOM 2413 CG GLU 158 34.768 52.396 15.325
ATOM 2414 2HG GLU 158 34.414 52.137 16.323
ATOM 2415 3HG GLU 158 33.855 52.471 14.735
ATOM 2416 CD GLU 158 35.616 51.243 14.745
ATOM 2417 OE1 GLU 158 36.318 50.563 15.478
ATOM 2418 OE2 GLU 158 35.517 50.983 13.521
ATOM 2419 C GLU 158 37.331 55.181 15.770
ATOM 2420 O GLU 158 38.509 55.258 15.446
ATOM 2421 OXT GLU 158 36.647 56.223 15.912
ATOM 2422 N MET 159 57.187 49.344 8.302
ATOM 2423 H1 MET 159 58.164 49.404 8.550
ATOM 2424 H2 MET 159 56.749 49.930 8.998
ATOM 2425 H3 MET 159 57.049 49.830 7.427
TER
ATOM 2426 CA MET 159 56.759 47.930 8.261
ATOM 2427 HA MET 159 55.672 47.924 8.186
ATOM 2428 CB MET 159 57.302 47.188 7.059
ATOM 2429 2HB MET 159 57.181 46.119 7.237
ATOM 2430 3HB MET 159 56.777 47.521 6.163
ATOM 2431 CG MET 159 58.769 47.282 6.818
ATOM 2432 2HG MET 159 59.243 47.481 7.780
ATOM 2433 3HG MET 159 58.914 46.273 6.432
ATOM 2434 SD MET 159 59.306 48.648 5.829
ATOM 2435 CE MET 159 61.028 48.239 5.783
ATOM 2436 1HE MET 159 61.399 48.021 6.784
ATOM 2437 2HE MET 159 61.062 47.360 5.139
ATOM 2438 3HE MET 159 61.561 49.085 5.350
ATOM 2439 C MET 159 57.279 47.251 9.593
ATOM 2440 O MET 159 58.409 47.411 10.022
........
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Received on Thu Feb 12 2004 - 15:53:00 PST
