AMBER Archive (2006)

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

From: Shuting Wei (gtg549i_at_mail.gatech.edu)
Date: Fri Sep 22 2006 - 16:42:04 CDT

Hello, Dr. Case,

Thank you for your answer. Yes, i prepared the prepin via
antechamber. I modified the prepin file as you suggested (attached),
but i still have the same error message, can you help to check if
there is anything wrong with my command lines? Thanks a lot!

> source leaprc.ff99
> loadamberprep polyamine.prepin
> loadamberprep polyamine.frcmod
> set PAM tail PAM.1.12
> desc PAM
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
!
!ABORTING.

Shuting Wei

At 05:01 PM 9/22/2006, you wrote:
>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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