On Fri, Sep 22, 2006, Shuting Wei wrote:
> UNIT name: PAM
> Head atom: .R<PAM 1>.A<C1 1>
> Tail atom: .R<PAM 1>.A<N4 12>
> Contents:
> R<PAM 1>
> > triPAM = sequence { PAM PAM PAM }
> ERROR: Comparing atoms N4, H14, H16, H18 to atoms C2, N4, H18, H14
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 121
> !FATAL: Message: Atom C2 is not in the first list
The chain designations in your prepin file are wrong:
0 0 2
This is a remark line
molecule.res
PAM INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C1 c3 M 3 2 1 1.540 111.208 180.000 -0.08780
5 H14 hc E 4 3 2 1.000 34.406 44.355 0.04659
6 H16 hc E 4 3 2 1.000 96.890 158.991 0.04807
7 H18 hc E 4 3 2 1.001 84.783 -92.070 0.04032
8 C2 c3 M 4 3 2 1.551 142.605 23.598 0.13869
9 O7 oh S 8 4 3 1.430 107.415 -46.730 -0.60387
10 H38 ho E 9 8 4 1.000 109.488 179.983 0.39551
11 H20 h1 E 8 4 3 1.000 106.317 75.674 0.04246
12 C3 c3 M 8 4 3 1.589 115.695 -167.699 0.14328
13 H22 h1 E 12 8 4 1.000 107.400 54.846 0.04261
14 H24 h1 E 12 8 4 1.001 107.377 172.554 0.03273
15 N4 n3 M 12 8 4 1.515 117.589 -66.372 -0.75230
16 C6 c3 3 15 12 8 1.470 108.039 -166.481 0.16544
17 H32 h1 E 16 15 12 1.000 109.432 -179.972 0.04469
18 H34 h1 E 16 15 12 1.000 109.455 60.072 0.04139
19 H36 h1 E 16 15 12 1.000 109.491 -59.999 0.00419
20 C5 c3 M 15 12 8 1.481 114.602 74.347 0.16334
^^^^^
Atom C5 must be of type "3", not M (it is not part of the mainchain that will
be linked to other groups.)
21 H26 h1 E 20 15 12 1.000 109.468 -179.981 0.04352
22 H28 h1 E 20 15 12 0.999 109.500 60.015 0.00487
23 H30 h1 E 20 15 12 1.000 109.485 -60.093 0.04630
Fixing this allowed me to use the sequence command without any problem.
Note: until you posted your prepin file, there is no way that anyone could
have seen this problem.
Note2: did you make this prepin via antechamber? That might indicate a
problem with that program...
...dac
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Received on Sun Sep 24 2006 - 06:07:20 PDT
