AMBER Archive (2006)

Subject: Re: AMBER: build a polymer with sequence command

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 22 2006 - 16:01:27 CDT

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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