AMBER Archive (2006)

Subject: AMBER: RE: Respgen segemtation fault

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Wed Apr 19 2006 - 12:10:11 CDT


Thanks for your reply Prof. Case. I tried what you suggested but that also ended in a segmentation fault. However, i didn`t have the tp.ac file in my $AMBERHOME/test/antechamber/tp directory, only a pdb file, so converted it using antechamber. Is this ok because this is what i have been doing with my input files? I have also listed below a copy of the .ac file i am using as the input for respgen, maybe this might provide some insight? The c compilers i have used are gcc and g++. Does this give you any more clues?

Many thanks in advance

Simon

CHARGE -2.00 ( -2 )
Formula: H29 C21 N7 O14 P2
ATOM 1 P1 MOL 1 -0.190 1.255 -0.928 0.000000 p5
ATOM 2 O1 MOL 1 -0.433 -0.201 -1.135 0.000000 o
ATOM 3 O2 MOL 1 0.548 2.010 -1.966 0.000000 o
ATOM 4 O3 MOL 1 0.626 1.400 0.484 0.000000 os
ATOM 5 C1 MOL 1 1.834 0.739 0.684 0.000000 c3
ATOM 6 C2 MOL 1 2.929 1.235 -0.258 0.000000 c3
ATOM 7 O4 MOL 1 4.196 1.043 0.405 0.000000 os
ATOM 8 C3 MOL 1 3.061 0.525 -1.627 0.000000 c3
ATOM 9 O5 MOL 1 3.155 1.452 -2.655 0.000000 oh
ATOM 10 C4 MOL 1 4.372 -0.260 -1.488 0.000000 c3
ATOM 11 O6 MOL 1 4.999 -0.475 -2.704 0.000000 oh
ATOM 12 C5 MOL 1 5.143 0.610 -0.496 0.000000 c3
ATOM 13 N1 MOL 1 6.164 -0.090 0.302 0.000000 na
ATOM 14 C6 MOL 1 6.321 0.023 1.659 0.000000 cc
ATOM 15 N2 MOL 1 7.342 -0.601 2.131 0.000000 nd
ATOM 16 C7 MOL 1 7.918 -1.173 1.019 0.000000 ca
ATOM 17 C8 MOL 1 9.051 -1.965 0.841 0.000000 ca
ATOM 18 N3 MOL 1 9.819 -2.366 1.885 0.000000 nh
ATOM 19 N4 MOL 1 9.382 -2.360 -0.382 0.000000 nb
ATOM 20 C9 MOL 1 8.597 -1.995 -1.388 0.000000 ca
ATOM 21 N5 MOL 1 7.510 -1.263 -1.353 0.000000 nb
ATOM 22 C10 MOL 1 7.202 -0.860 -0.119 0.000000 ca
ATOM 23 O7 MOL 1 -1.560 1.930 -0.529 0.000000 os
ATOM 24 P2 MOL 1 -2.307 3.239 0.133 0.000000 p5
ATOM 25 O8 MOL 1 -2.968 3.981 -0.945 0.000000 o
ATOM 26 O9 MOL 1 -1.440 3.851 1.150 0.000000 o
ATOM 27 O10 MOL 1 -3.492 2.392 0.909 0.000000 os
ATOM 28 C11 MOL 1 -3.497 2.152 2.283 0.000000 c3
ATOM 29 C12 MOL 1 -3.474 0.666 2.610 0.000000 c3
ATOM 30 O11 MOL 1 -4.659 0.019 2.147 0.000000 os
ATOM 31 C13 MOL 1 -2.325 -0.096 1.969 0.000000 c3
ATOM 32 O12 MOL 1 -1.985 -1.194 2.791 0.000000 oh
ATOM 33 C14 MOL 1 -2.963 -0.618 0.685 0.000000 c3
ATOM 34 O13 MOL 1 -2.313 -1.740 0.174 0.000000 oh
ATOM 35 C15 MOL 1 -4.368 -0.950 1.178 0.000000 c3
ATOM 36 N6 MOL 1 -5.408 -0.969 0.179 0.000000 nh
ATOM 37 C16 MOL 1 -6.258 -2.006 0.106 0.000000 c2
ATOM 38 C17 MOL 1 -7.339 -2.079 -0.703 0.000000 ce
ATOM 39 C18 MOL 1 -8.223 -3.243 -0.692 0.000000 c
ATOM 40 O14 MOL 1 -9.042 -3.464 -1.553 0.000000 o
ATOM 41 N7 MOL 1 -8.107 -4.138 0.366 0.000000 n
ATOM 42 C19 MOL 1 -7.619 -0.982 -1.707 0.000000 c3
ATOM 43 C20 MOL 1 -6.390 -0.082 -1.866 0.000000 c3
ATOM 44 C21 MOL 1 -5.780 0.262 -0.512 0.000000 c3
ATOM 45 H1 MOL 1 1.708 -0.336 0.592 0.000000 h1
ATOM 46 H2 MOL 1 2.144 0.958 1.698 0.000000 h1
ATOM 47 H3 MOL 1 2.791 2.292 -0.424 0.000000 h1
ATOM 48 H4 MOL 1 2.234 -0.150 -1.797 0.000000 h1
ATOM 49 H5 MOL 1 2.272 1.834 -2.703 0.000000 ho
ATOM 50 H6 MOL 1 4.153 -1.200 -0.981 0.000000 h1
ATOM 51 H7 MOL 1 5.836 -0.899 -2.549 0.000000 ho
ATOM 52 H8 MOL 1 5.624 1.433 -1.015 0.000000 h2
ATOM 53 H9 MOL 1 5.622 0.590 2.233 0.000000 h5
ATOM 54 H10 MOL 1 10.728 -2.702 1.664 0.000000 hn
ATOM 55 H11 MOL 1 8.898 -2.346 -2.358 0.000000 h5
ATOM 56 H12 MOL 1 -4.409 2.574 2.699 0.000000 h1
ATOM 57 H13 MOL 1 -2.651 2.632 2.757 0.000000 h1
ATOM 58 H14 MOL 1 -3.437 0.555 3.689 0.000000 h1
ATOM 59 H15 MOL 1 -1.459 0.525 1.792 0.000000 h1
ATOM 60 H16 MOL 1 -1.641 -1.854 2.200 0.000000 ho
ATOM 61 H17 MOL 1 -2.994 0.171 -0.044 0.000000 h1
ATOM 62 H18 MOL 1 -1.609 -1.388 -0.388 0.000000 ho
ATOM 63 H19 MOL 1 -4.350 -1.936 1.629 0.000000 h2
ATOM 64 H20 MOL 1 -6.002 -2.834 0.740 0.000000 ha
ATOM 65 H21 MOL 1 -8.866 -4.785 0.385 0.000000 hn
ATOM 66 H22 MOL 1 -8.477 -0.387 -1.395 0.000000 hc
ATOM 67 H23 MOL 1 -7.890 -1.425 -2.659 0.000000 hc
ATOM 68 H24 MOL 1 -5.639 -0.586 -2.467 0.000000 hc
ATOM 69 H25 MOL 1 -4.912 0.890 -0.618 0.000000 h1
ATOM 70 H26 MOL 1 9.709 -1.879 2.746 0.000000 hn
ATOM 71 H27 MOL 1 -7.889 -3.756 1.258 0.000000 hn
ATOM 72 H28 MOL 1 -6.496 0.810 0.096 0.000000 h1
ATOM 73 H29 MOL 1 -6.652 0.837 -2.382 0.000000 hc
BOND 1 1 2 9 P1 O1
BOND 2 1 3 9 P1 O2
BOND 3 1 4 1 P1 O3
BOND 4 1 23 1 P1 O7
BOND 5 4 5 1 O3 C1
BOND 6 5 6 1 C1 C2
BOND 7 5 45 1 C1 H1
BOND 8 5 46 1 C1 H2
BOND 9 6 7 1 C2 O4
BOND 10 6 8 1 C2 C3
BOND 11 6 47 1 C2 H3
BOND 12 7 12 1 O4 C5
BOND 13 8 9 1 C3 O5
BOND 14 8 10 1 C3 C4
BOND 15 8 48 1 C3 H4
BOND 16 9 49 1 O5 H5
BOND 17 10 11 1 C4 O6
BOND 18 10 12 1 C4 C5
BOND 19 10 50 1 C4 H6
BOND 20 11 51 1 O6 H7
BOND 21 12 13 1 C5 N1
BOND 22 12 52 1 C5 H8
BOND 23 13 14 7 N1 C6
BOND 24 13 22 7 N1 C10
BOND 25 14 15 8 C6 N2
BOND 26 14 53 1 C6 H9
BOND 27 15 16 7 N2 C7
BOND 28 16 17 1 C7 C8
BOND 29 16 22 8 C7 C10
BOND 30 17 18 1 C8 N3
BOND 31 17 19 2 C8 N4
BOND 32 18 54 1 N3 H10
BOND 33 18 70 1 N3 H26
BOND 34 19 20 1 N4 C9
BOND 35 20 21 2 C9 N5
BOND 36 20 55 1 C9 H11
BOND 37 21 22 1 N5 C10
BOND 38 23 24 1 O7 P2
BOND 39 24 25 9 P2 O8
BOND 40 24 26 9 P2 O9
BOND 41 24 27 1 P2 O10
BOND 42 27 28 1 O10 C11
BOND 43 28 29 1 C11 C12
BOND 44 28 56 1 C11 H12
BOND 45 28 57 1 C11 H13
BOND 46 29 30 1 C12 O11
BOND 47 29 31 1 C12 C13
BOND 48 29 58 1 C12 H14
BOND 49 30 35 1 O11 C15
BOND 50 31 32 1 C13 O12
BOND 51 31 33 1 C13 C14
BOND 52 31 59 1 C13 H15
BOND 53 32 60 1 O12 H16
BOND 54 33 34 1 C14 O13
BOND 55 33 35 1 C14 C15
BOND 56 33 61 1 C14 H17
BOND 57 34 62 1 O13 H18
BOND 58 35 36 1 C15 N6
BOND 59 35 63 1 C15 H19
BOND 60 36 37 1 N6 C16
BOND 61 36 44 1 N6 C21
BOND 62 37 38 2 C16 C17
BOND 63 37 64 1 C16 H20
BOND 64 38 39 1 C17 C18
BOND 65 38 42 1 C17 C19
BOND 66 39 40 2 C18 O14
BOND 67 39 41 1 C18 N7
BOND 68 41 65 1 N7 H21
BOND 69 41 71 1 N7 H27
BOND 70 42 43 1 C19 C20
BOND 71 42 66 1 C19 H22
BOND 72 42 67 1 C19 H23
BOND 73 43 44 1 C20 C21
BOND 74 43 68 1 C20 H24
BOND 75 43 73 1 C20 H29
BOND 76 44 69 1 C21 H25
BOND 77 44 72 1 C21 H28

From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Thu 13/04/2006 19:46
To: amber_at_scripps.edu
Subject: Re: AMBER: Respgen segemtation fault

On Thu, Apr 13, 2006, Simon Whitehead wrote:
>
> I have encountered difficulty when trying to use respgen in Amber 8,
> everytime i invoke it there is a segmentation fault. I have tried it on two
> different builds (P4 and athlon linux machines both complied with ifort
> ver9) with several different input files but the result is the same. The
> antechamber test runs with no problems but still respgen does not work.
>

We will need more information, probably the input file you used. You can
go to $AMBERHOME/test/antechamber/tp and try this:

     respgen -i tp.ac -o foo -f resp1

This works fine for me, so that would start to see if the problem is in the
input file or in your version of respgen. (I've tried several other input
files, and they all work as well.)

[Note also that respgen is a C program, so the key item is not which fortran
compiler you used, but which C compiler...]

...regards...dac
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