AMBER Archive (2002)

Subject: Segmentation fault

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Tue Jul 23 2002 - 14:44:58 CDT

Dear Amber users,

What does it mean with "segmentation fault"? I try to replace one residue (Lysine) with the modified one and suddenly xLeap stops running and jumps out with message: "segmentation fault". The atom types of modified Lysine are correct (checked by "check unit"), so what's going wrong? I send the .lib of modified Lysine and you can try to do it using any protein and just change one Lysine with this one (use any text editor). Sorry to take your time, but I really don't understand what's going on.

Best regards,
bimo
ITB-Stuttgart

===============================

!!index array str
 "OCT"
!entry.OCT.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
 "N" "N" 0 1 131072 18 7 -0.416000
 "H" "H" 0 1 131072 19 1 0.272000
 "CA" "CT" 0 1 131072 20 6 0.105000
 "C" "C" 0 1 131072 21 6 0.597000
 "O" "O" 0 1 131072 22 8 -0.568000
 "H10" "H1" 0 1 131072 45 1 0.122000
 "C8" "CT" 0 1 131072 46 6 -0.411000
 "H11" "HC" 0 1 131072 47 1 0.090000
 "H12" "HC" 0 1 131072 48 1 0.090000
 "C9" "CT" 0 1 131072 49 6 0.297000
 "H13" "HC" 0 1 131072 50 1 -0.033000
 "H14" "HC" 0 1 131072 51 1 -0.033000
 "C10" "CT" 0 1 131072 52 6 -0.047000
 "H15" "HC" 0 1 131072 53 1 0.013000
 "H16" "HC" 0 1 131072 54 1 0.013000
 "C11" "CT" 0 1 131072 55 6 -0.285000
 "H17" "HP" 0 1 131072 56 1 0.173000
 "H18" "HP" 0 1 131072 57 1 0.173000
 "N3" "N3" 0 1 131072 58 7 -0.178000
 "H19" "H" 0 1 131072 59 1 0.477000
 "H20" "H" 0 1 131072 60 1 0.477000
 "C12" "CT" 0 1 131072 61 6 -0.773000
 "H36" "HP" 0 1 131072 62 1 0.259000
 "H37" "HP" 0 1 131072 63 1 0.259000
 "C13" "CT" 0 1 131072 64 6 -0.011000
 "H34" "HC" 0 1 131072 65 1 0.125000
 "H35" "HC" 0 1 131072 66 1 0.125000
 "C14" "CT" 0 1 131072 67 6 -0.028000
 "H32" "HC" 0 1 131072 68 1 0.054000
 "H33" "HC" 0 1 131072 69 1 0.054000
 "C15" "CT" 0 1 131072 70 6 -0.055000
 "H30" "HC" 0 1 131072 71 1 0.010000
 "H31" "HC" 0 1 131072 72 1 0.010000
 "C16" "CT" 0 1 131072 73 6 0.011000
 "H28" "HC" 0 1 131072 74 1 -0.006000
 "H29" "HC" 0 1 131072 75 1 -0.006000
 "C17" "CT" 0 1 131072 76 6 0.004000
 "H26" "HC" 0 1 131072 77 1 0.012000
 "H27" "HC" 0 1 131072 78 1 0.012000
 "C18" "CT" 0 1 131072 79 6 0.015000
 "H24" "HC" 0 1 131072 80 1 0.012000
 "H25" "HC" 0 1 131072 81 1 0.012000
 "C19" "CT" 0 1 131072 82 6 -0.111000
 "H21" "HC" 0 1 131072 83 1 0.028000
 "H22" "HC" 0 1 131072 84 1 0.028000
 "H23" "HC" 0 1 131072 85 1 0.028000
!entry.OCT.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N2" "N" 0 -1 0.0
"H9" "H" 0 -1 0.0
"C6" "C" 0 -1 0.0
"C7" "C" 0 -1 0.0
"O4" "O" 0 -1 0.0
"H10" "H" 0 -1 0.0
"C8" "C" 0 -1 0.0
"H11" "H" 0 -1 0.0
"H12" "H" 0 -1 0.0
"C9" "C" 0 -1 0.0
"H13" "H" 0 -1 0.0
"H14" "H" 0 -1 0.0
"C10" "C" 0 -1 0.0
"H15" "H" 0 -1 0.0
"H16" "H" 0 -1 0.0
"C11" "C" 0 -1 0.0
"H17" "H" 0 -1 0.0
"H18" "H" 0 -1 0.0
"N3" "N" 0 -1 0.0
"H19" "H" 0 -1 0.0
"H20" "H" 0 -1 0.0
"C12" "C" 0 -1 0.0
"H36" "H" 0 -1 0.0
"H37" "H" 0 -1 0.0
"C13" "C" 0 -1 0.0
"H34" "H" 0 -1 0.0
"H35" "H" 0 -1 0.0
"C14" "C" 0 -1 0.0
"H32" "H" 0 -1 0.0
"H33" "H" 0 -1 0.0
"C15" "C" 0 -1 0.0
"H30" "H" 0 -1 0.0
"H31" "H" 0 -1 0.0
"C16" "C" 0 -1 0.0
"H28" "H" 0 -1 0.0
"H29" "H" 0 -1 0.0
"C17" "C" 0 -1 0.0
"H26" "H" 0 -1 0.0
"H27" "H" 0 -1 0.0
"C18" "C" 0 -1 0.0
"H24" "H" 0 -1 0.0
"H25" "H" 0 -1 0.0
"C19" "C" 0 -1 0.0
"H21" "H" 0 -1 0.0
"H22" "H" 0 -1 0.0
"H23" "H" 0 -1 0.0
!entry.OCT.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.OCT.unit.childsequence single int
 2
!entry.OCT.unit.connect array int
 1
 4
!entry.OCT.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
3 4 1
3 6 1
3 7 1
4 5 1
7 8 1
7 9 1
7 10 1
10 11 1
10 12 1
10 13 1
13 14 1
13 15 1
13 16 1
16 17 1
16 18 1
16 19 1
19 20 1
19 21 1
19 22 1
22 23 1
22 24 1
22 25 1
25 26 1
25 27 1
25 28 1
28 29 1
28 30 1
28 31 1
31 32 1
31 33 1
31 34 1
34 35 1
34 36 1
34 37 1
37 38 1
37 39 1
37 40 1
40 41 1
40 42 1
40 43 1
43 44 1
43 45 1
43 46 1
!entry.OCT.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
"R" 1 "A" 32
"R" 1 "A" 33
"R" 1 "A" 34
"R" 1 "A" 35
"R" 1 "A" 36
"R" 1 "A" 37
"R" 1 "A" 38
"R" 1 "A" 39
"R" 1 "A" 40
"R" 1 "A" 41
"R" 1 "A" 42
"R" 1 "A" 43
"R" 1 "A" 44
"R" 1 "A" 45
"R" 1 "A" 46
!entry.OCT.unit.name single str
 "OCT"
!entry.OCT.unit.positions table dbl x dbl y dbl z
6.041670 3.945920 -4.007682
6.799912 3.260403 -3.865699
6.403326 5.143310 -4.815507
7.737809 4.825846 -5.558455
7.788235 4.608843 -6.754890
5.638363 5.267821 -5.586206
6.488863 6.466608 -4.001441
6.910479 7.221465 -4.663523
7.171155 6.354884 -3.161358
5.111989 6.962021 -3.499453
4.365588 6.757669 -4.264221
5.146971 8.042362 -3.375423
4.687085 6.333107 -2.149147
5.186950 6.853869 -1.336430
4.989130 5.290365 -2.094118
3.164590 6.435285 -1.907086
2.784850 7.408368 -2.222027
2.917937 6.289867 -0.854329
2.409737 5.368087 -2.674901
2.574541 4.406347 -2.186868
2.838038 5.220863 -3.619987
0.928090 5.671326 -2.779899
0.549127 5.723610 -1.759235
0.832200 6.657449 -3.239061
0.172138 4.604974 -3.599824
0.568278 4.590707 -4.614117
0.339927 3.624561 -3.158937
-1.341147 4.914085 -3.637821
-1.726345 4.933393 -2.619405
-1.493943 5.904414 -4.061666
-2.121274 3.869535 -4.466882
-1.729279 3.855259 -5.482784
-1.956484 2.881142 -4.043009
-3.635401 4.169630 -4.502882
-4.022349 4.185913 -3.486147
-3.794246 5.161317 -4.923889
-4.417264 3.128427 -5.332655
-4.028226 3.113132 -6.349679
-4.255357 2.137313 -4.911467
-5.932769 3.426587 -5.369672
-6.320944 3.442890 -4.352335
-6.093555 4.416923 -5.790535
-6.714667 2.388308 -6.197496
-7.774239 2.626357 -6.203517
-6.363768 2.371952 -7.224057
-6.591761 1.393189 -5.780328
!entry.OCT.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 60 0 0 0 0
!entry.OCT.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
 "OCT" 1 86 1 "?" 0
!entry.OCT.unit.residuesPdbSequenceNumber array int
 0
!entry.OCT.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.OCT.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0 

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