Dear Amber users,
This question isn't related to AMBER. I am doing nucleic acid
dynamics and trying to use MD Toolchest 1.0 to analyze the structures in
trajectories. However, MD Toolchest doesn't quite cooperate with me. My
question is how I should 'massage' my PDB file to suit MD Toolchest's
taste. It looks to me Toolchest requires 3-letter residue name and '*'
instead of '. But it still complains about this " Strand: 2 Unit: 1
(CYT 40) atom C6 absent". Here is what I have in my PDB file for
CYT(BTW, this PDB file was already amber_massaged).
ATOM P CYT 14 7.601 -5.295 2.873
ATOM O1P CYT 14 9.047 -5.346 2.581
ATOM O2P CYT 14 7.197 -4.416 3.997
ATOM O5* CYT 14 6.793 -4.883 1.561
ATOM C5* CYT 14 6.722 -5.825 0.460
ATOM C4* CYT 14 6.709 -5.076 -0.852
ATOM O4* CYT 14 5.348 -4.601 -1.107
ATOM C1* CYT 14 5.281 -3.204 -0.895
ATOM N1 CYT 14 4.158 -2.942 0.046
ATOM C6 CYT 14 4.315 -3.077 1.388
ATOM C5 CYT 14 3.292 -2.833 2.251
ATOM C4 CYT 14 2.044 -2.440 1.672
ATOM N4 CYT 14 1.000 -2.192 2.447
ATOM H41 CYT 14 0.121 -1.911 2.035
ATOM H42 CYT 14 1.083 -2.282 3.450
ATOM N3 CYT 14 1.899 -2.308 0.348
ATOM C2 CYT 14 2.933 -2.553 -0.493
ATOM O2 CYT 14 2.829 -2.439 -1.721
ATOM C3* CYT 14 7.566 -3.814 -0.922
ATOM C2* CYT 14 6.636 -2.742 -0.378
ATOM O3* CYT 14 7.929 -3.483 -2.261
Here is the same residue in dickerson.pdb in example directory.
ATOM P CYT A 15 -13.500 -9.554 0.591
ATOM O1P CYT A 15 -12.713 -9.552 1.839
ATOM O2P CYT A 15 -13.686 -10.841 -0.109
ATOM NA CYT A 15 -11.919 -12.934 2.032
ATOM O5* CYT A 15 -12.904 -8.490 -0.440
ATOM C5* CYT A 15 -13.516 -8.278 -1.727
ATOM C4* CYT A 15 -12.866 -7.041 -2.279
ATOM O4* CYT A 15 -12.986 -6.023 -1.288
ATOM C1* CYT A 15 -12.084 -5.016 -1.678
ATOM N1 CYT A 15 -11.743 -4.333 -0.421
ATOM C6 CYT A 15 -11.501 -5.077 0.699
ATOM C2 CYT A 15 -11.756 -2.976 -0.394
ATOM O2 CYT A 15 -11.969 -2.383 -1.446
ATOM N3 CYT A 15 -11.546 -2.334 0.761
ATOM C4 CYT A 15 -11.319 -3.009 1.878
ATOM N4 CYT A 15 -11.131 -2.339 3.061
ATOM H41 CYT A 15 -10.964 -2.846 3.908
ATOM H42 CYT A 15 -11.171 -1.334 3.052
ATOM C5 CYT A 15 -11.263 -4.397 1.893
ATOM C2* CYT A 15 -10.909 -5.716 -2.313
ATOM C3* CYT A 15 -11.366 -7.152 -2.442
ATOM O3* CYT A 15 -11.040 -7.738 -3.703
Besides the difference in the column used for residue name, the atom
order is also different. What does matter? (The sodium shouldn't be a
problem,should it?)
Thanks.
--
Guanglei Cui
State University of New York
Department of Chemistry
Stony Brook, 11794-3400
Received on Wed May 31 2000 - 10:16:32 PDT
