AMBER Archive (2008)

Subject: AMBER: xleap segmentation fault on SaveAmberParm

From: Brendan Duggan (bmduggan_at_musc.edu)
Date: Tue Apr 15 2008 - 14:15:46 CDT

I tried to post this a few weeks ago but it seems it never made it to
the mailing list. My apologies if this is a repeat.

I've been trying to create a prmtop file for a sphingolipid, however
xleap (Amber9 and AmberTools versions) crashes and issues a
"Segmentation fault" when I issue the SaveAmberParm command. The
AmberTools version of xleap gives a bit more information on crashing.
Here's the output I get:

> /opt/amber10/bin/xleap -s -f glccer.leaprc
-I: Adding /opt/amber10/dat/leap/prep to search path.
-I: Adding /opt/amber10/dat/leap/lib to search path.
-I: Adding /opt/amber10/dat/leap/parm to search path.
-I: Adding /opt/amber10/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source glccer.leaprc.
/opt/amber10/bin/xleap: line 9: 13401 Segmentation
Fault /opt/amber10/bin/xaLeap -I/opt/amber10/dat/leap/prep -
I/opt/amber10/dat/leap/lib -I/opt/amber10/dat/leap/parm -
I/opt/amber10/dat/leap/cmd $*

The number between "line 9" and "Segmentation fault" changes with each
crash. The file "glccer.leaprc" is as follows:

source leaprc.gaff

# load residues
LoadAmberPrep stearate.prepin
LoadAmberPrep sphingosine.prepin
LoadAmberPrep glucose.prepin

# set connection atoms to link residues
set STE.1 connect1 STE.1.C1
set STE tail STE.1.C1
set SPH.1 connect0 SPH.1.N2
set SPH.1 connect1 SPH.1.O1
set SPH head SPH.1.N2
set SPH tail SPH.1.O1

# combine residues into one new molecule
GLCCER = sequence { STE SPH GLC }

# correct incorect Glucose linkage
deletebond GLCCER.2.O1 GLCCER.3.O4
bond GLCCER.2.O1 GLCCER.3.C1

# remove atoms eliminated in linkages
remove GLCCER GLCCER.STE.O1'
remove GLCCER GLCCER.STE.HO1
remove GLCCER GLCCER.SPH.HN23
remove GLCCER GLCCER.SPH.HO1
remove GLCCER GLCCER.GLC.H11

# make double bond b/w SPH C8 and C9
remove GLCCER GLCCER.SPH.H83
remove GLCCER GLCCER.SPH.H93

# make hydroxyl at STE C2
set GLCCER.STE.H23 name O2
set GLCCER.STE.O2 element O
set GLCCER.STE.O2 type oh
set GLCCER.STE.O2 charge -0.62703
h1 = CreateAtom HO2 ho 0.417
set h1 element H
add GLCCER h1
bond GLCCER.STE.O2 h1

# save prmtop and inpcrd files
SaveAmberParm GLCCER glccer.prmtop glccer.inpcrd

The prep files stearate.prepin, sphingosine.prepin and glucose.prepin
were prepared using GAFF and are attached.

Can anyone tell me what I'm doing wrong?

Brendan 

-- 
Brendan Duggan <bmduggan_at_musc.edu>
Medical University of South Carolina

    0 0 2

This is a remark line
molecule.res
STE 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 O1 o M 3 2 1 1.540 111.208 180.000 -0.55500
   5 C1 c M 4 3 2 1.209 161.582 94.054 0.63403
   6 O1' oh S 5 4 3 1.308 120.864 -87.339 -0.60719
   7 HO1 ho E 6 5 4 0.972 106.599 -87.072 0.44353
   8 C2 c3 M 5 4 3 1.520 121.024 68.118 -0.12516
   9 H23 hc E 8 5 4 1.093 107.844 84.777 0.08012
  10 H22 hc E 8 5 4 1.093 108.276 -30.740 0.08063
  11 C3 c3 M 8 5 4 1.547 115.491 -152.962 -0.07768
  12 H33 hc E 11 8 5 1.093 109.699 67.655 0.05153
  13 H32 hc E 11 8 5 1.094 110.854 -51.447 0.06270
  14 C4 c3 M 11 8 5 1.534 109.505 -171.220 -0.08011
  15 H43 hc E 14 11 8 1.093 109.217 61.876 0.04084
  16 H42 hc E 14 11 8 1.093 109.622 -55.879 0.04096
  17 C5 c3 M 14 11 8 1.536 111.761 -177.327 -0.07844
  18 H53 hc E 17 14 11 1.093 110.095 60.314 0.04212
  19 H52 hc E 17 14 11 1.094 110.207 -58.552 0.04279
  20 C6 c3 M 17 14 11 1.535 108.751 -179.103 -0.07933
  21 H63 hc E 20 17 14 1.094 109.580 59.350 0.03990
  22 H62 hc E 20 17 14 1.093 109.609 -58.543 0.03997
  23 C7 c3 M 20 17 14 1.532 110.999 -179.631 -0.07881
  24 H73 hc E 23 20 17 1.093 109.780 59.107 0.04036
  25 H72 hc E 23 20 17 1.093 109.868 -59.357 0.04043
  26 C8 c3 M 23 20 17 1.535 109.727 179.869 -0.07921
  27 H83 hc E 26 23 20 1.093 109.874 59.241 0.03956
  28 H82 hc E 26 23 20 1.094 109.844 -59.084 0.03961
  29 C9 c3 M 26 23 20 1.533 109.934 -179.829 -0.07877
  30 H93 hc E 29 26 23 1.093 109.739 59.030 0.03990
  31 H92 hc E 29 26 23 1.093 109.661 -59.183 0.03991
  32 C10 c3 M 29 26 23 1.533 110.188 179.956 -0.07921
  33 H10 hc E 32 29 26 1.094 109.820 59.151 0.03945
  34 H19 hc E 32 29 26 1.094 109.788 -59.217 0.03947
  35 C11 c3 M 32 29 26 1.534 109.816 179.978 -0.07874
  36 H11 hc E 35 32 29 1.094 109.671 59.112 0.03972
  37 H20 hc E 35 32 29 1.093 109.685 -59.124 0.03972
  38 C12 c3 M 35 32 29 1.533 110.104 179.948 -0.07918
  39 H12 hc E 38 35 32 1.094 109.645 59.161 0.03940
  40 H21 hc E 38 35 32 1.093 109.717 -59.091 0.03941
  41 C13 c3 M 38 35 32 1.535 110.035 179.963 -0.07878
  42 H13 hc E 41 38 35 1.093 109.651 59.134 0.03962
  43 H24 hc E 41 38 35 1.093 109.671 -59.028 0.03961
  44 C14 c3 M 41 38 35 1.535 110.155 -179.978 -0.07911
  45 H14 hc E 44 41 38 1.094 109.587 59.100 0.03939
  46 H25 hc E 44 41 38 1.093 109.598 -58.966 0.03941
  47 C15 c3 M 44 41 38 1.537 110.342 -179.944 -0.07894
  48 H15 hc E 47 44 41 1.093 109.574 58.956 0.03941
  49 H26 hc E 47 44 41 1.094 109.522 -58.979 0.03940
  50 C16 c3 M 47 44 41 1.537 110.359 -179.957 -0.07936
  51 H16 hc E 50 47 44 1.093 109.500 58.880 0.03935
  52 H27 hc E 50 47 44 1.093 109.437 -58.929 0.03936
  53 C17 c3 M 50 47 44 1.539 110.741 180.000 -0.08010
  54 H17 hc E 53 50 47 1.094 109.740 59.028 0.03838
  55 H28 hc E 53 50 47 1.093 109.757 -59.069 0.03838
  56 C18 c3 M 53 50 47 1.538 110.678 179.941 -0.09258
  57 H18 hc E 56 53 50 1.092 110.293 179.985 0.03239
  58 H29 hc E 56 53 50 1.093 110.498 60.111 0.03245
  59 H30 hc E 56 53 50 1.093 110.544 -60.092 0.03247

LOOP

IMPROPER
   C2 O1 C1 O1'

DONE
STOP


    0 0 2

This is a remark line
molecule.res
SPH 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 O1 oh M 3 2 1 1.540 111.208 180.000 -0.60427
   5 HO1 ho E 4 3 2 0.960 146.453 -39.723 0.40400
   6 C1 c3 M 4 3 2 1.430 37.396 -28.247 0.12528
   7 H13 h1 E 6 4 3 1.089 109.446 -80.575 0.03390
   8 H12 h1 E 6 4 3 1.088 109.435 159.510 0.02476
   9 C2 c3 M 6 4 3 1.527 109.509 39.458 0.14403
  10 N2 n3 B 9 6 4 1.496 109.483 -60.018 -0.91489
  11 HN22 hn E 10 9 6 1.035 109.453 59.999 0.36693
  12 HN23 hn E 10 9 6 1.010 109.444 179.962 0.35592
  13 H23 h1 E 9 6 4 1.088 109.501 59.944 0.04374
  14 C3 c3 M 9 6 4 1.528 109.489 -179.969 0.17611
  15 O3 oh S 14 9 6 1.431 109.463 -60.025 -0.59658
  16 HO3 ho E 15 14 9 0.970 109.940 59.958 0.39880
  17 H33 h1 E 14 9 6 1.088 109.481 59.987 0.05040
  18 C4 c2 M 14 9 6 1.511 109.473 -179.976 -0.17939
  19 H43 ha E 18 14 9 1.079 120.006 59.938 0.14049
  20 C5 c2 M 18 14 9 1.340 119.956 -120.027 -0.15788
  21 H53 ha E 20 18 14 1.080 120.022 -0.051 0.13194
  22 C6 c3 M 20 18 14 1.510 119.981 -179.989 -0.05084
  23 H62 hc E 22 20 18 1.088 109.463 -60.043 0.04774
  24 H63 hc E 22 20 18 1.088 109.500 60.010 0.04835
  25 C7 c3 M 22 20 18 1.529 109.474 179.978 -0.07674
  26 H72 hc E 25 22 20 1.088 109.490 -59.987 0.04458
  27 H73 hc E 25 22 20 1.089 109.434 60.010 0.04136
  28 C8 c3 M 25 22 20 1.528 109.467 179.946 -0.07977
  29 H82 hc E 28 25 22 1.088 109.519 -59.951 0.03918
  30 H83 hc E 28 25 22 1.089 109.439 60.067 0.04051
  31 C9 c3 M 28 25 22 1.529 109.467 180.000 -0.07885
  32 H92 hc E 31 28 25 1.088 109.457 -59.963 0.04043
  33 H93 hc E 31 28 25 1.088 109.429 60.043 0.03993
  34 C10 c3 M 31 28 25 1.528 109.452 -179.964 -0.07912
  35 H102 hc E 34 31 28 1.088 109.497 -59.974 0.03943
  36 H103 hc E 34 31 28 1.090 109.490 60.020 0.03973
  37 C11 c3 M 34 31 28 1.529 109.452 -180.000 -0.07891
  38 H112 hc E 37 34 31 1.088 109.457 -59.999 0.03976
  39 H113 hc E 37 34 31 1.088 109.429 60.007 0.03961
  40 C12 c3 M 37 34 31 1.528 109.452 180.000 -0.07908
  41 H122 hc E 40 37 34 1.097 108.513 -59.571 0.03942
  42 H123 hc E 40 37 34 1.090 109.490 60.020 0.03956
  43 C13 c3 M 40 37 34 1.529 109.452 -180.000 -0.07889
  44 H132 hc E 43 40 37 1.088 109.490 -59.969 0.03958
  45 H133 hc E 43 40 37 1.088 109.429 60.007 0.03951
  46 C14 c3 M 43 40 37 1.528 109.475 -179.987 -0.07903
  47 H142 hc E 46 43 40 1.089 109.421 -59.996 0.03941
  48 H143 hc E 46 43 40 1.089 109.310 59.810 0.03946
  49 C15 c3 M 46 43 40 1.528 109.458 -179.987 -0.07898
  50 H152 hc E 49 46 43 1.088 109.488 -59.993 0.03937
  51 H153 hc E 49 46 43 1.089 109.453 60.014 0.03935
  52 C16 c3 M 49 46 43 1.528 109.473 179.964 -0.07935
  53 H162 hc E 52 49 46 1.088 109.451 -59.941 0.03936
  54 H163 hc E 52 49 46 1.089 109.402 60.001 0.03939
  55 C17 c3 M 52 49 46 1.527 109.477 179.964 -0.08008
  56 H172 hc E 55 52 49 1.088 109.516 -59.938 0.03836
  57 H173 hc E 55 52 49 1.089 109.422 60.067 0.03836
  58 C18 c3 M 55 52 49 1.526 109.479 179.995 -0.09256
  59 H181 hc E 58 55 52 1.088 109.518 -179.964 0.03229
  60 H183 hc E 58 55 52 1.090 109.446 60.045 0.03245
  61 H182 hc E 58 55 52 1.091 109.282 -59.882 0.03243

LOOP

IMPROPER
   C5 C3 C4 H43
   C4 C6 C5 H53

DONE
STOP


    0 0 2

This is a remark line
molecule.res
GLC 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 O4 oh M 3 2 1 1.540 111.208 180.000 -0.60225
   5 HO4 ho E 4 3 2 0.976 17.354 87.639 0.42644
   6 C4 c3 M 4 3 2 1.438 107.438 179.165 0.12075
   7 H4 h1 E 6 4 3 1.096 109.108 -53.872 0.06355
   8 C3 c3 M 6 4 3 1.541 110.616 65.907 0.07220
   9 H3 h1 E 8 6 4 1.096 109.375 53.256 0.04873
  10 O3 oh S 8 6 4 1.435 110.023 -66.986 -0.60620
  11 HO3 ho E 10 8 6 0.978 107.199 -176.130 0.42392
  12 C2 c3 M 8 6 4 1.555 110.801 173.140 0.06992
  13 H2 h1 E 12 8 6 1.096 108.909 66.578 0.10314
  14 O2 oh S 12 8 6 1.431 109.495 -173.337 -0.58982
  15 HO2 ho E 14 12 8 0.978 109.062 60.195 0.40220
  16 C1 c3 M 12 8 6 1.546 110.582 -52.042 0.09978
  17 H1 h1 E 16 12 8 1.096 109.931 173.596 0.08705
  18 H11 h1 E 16 12 8 1.095 110.475 -65.989 0.03314
  19 O5 os M 16 12 8 1.444 109.498 54.119 -0.39649
  20 C5 c3 M 19 16 12 1.457 115.702 -60.807 0.09989
  21 H5 h1 E 20 19 16 1.094 108.748 -58.323 0.06043
  22 C6 c3 M 20 19 16 1.541 109.548 -178.684 0.13717
  23 H61 h1 E 22 20 19 1.096 108.846 -58.583 0.08874
  24 H62 h1 E 22 20 19 1.095 109.550 -176.681 0.04716
  25 O6 oh M 22 20 19 1.435 112.051 62.562 -0.59107
  26 HO6 ho E 25 22 20 0.974 108.733 77.894 0.40163

LOOP
   C5 C4

IMPROPER

DONE
STOP

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