Re: AMBER: mm_pbsa segmentation faults

From: Ray Luo <rluo.uci.edu>
Date: Tue, 26 Sep 2006 09:29:26 -0700

Thomas,

Your files work fine on my local system. I don't have any seg fault
problem. On what platform did it occur? My system is a Dell PE1850/Dual
Xeon 3.0GHz/3GB with FC5/ifc9.0.

All the best,
Ray

Thomas Steinbrecher wrote:

> Dear Dr. Luo,
>
> thanks for looking into this, please find attached the contents of one
> of my mm_pbsa directories (the prm file is supposed to be in the
> parent directory). I am sending you files for a ligand, cause they are
> smallest.
>
> I'd be very interested to hear if you see the same behaviour or if the
> problem lies with my machine.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
>------------------------------------------------------------------------
>
>%VERSION VERSION_STAMP = V0001.000 DATE = 08/22/06 15:31:34
>%FLAG TITLE
>%FORMAT(20a4)
>
>%FLAG POINTERS
>%FORMAT(10I8)
> 52 10 28 26 63 35 121 54 0 0
> 300 1 26 35 54 12 22 12 10 0
> 0 0 0 0 0 0 0 0 52 0
> 0
>%FLAG ATOM_NAME
>%FORMAT(20a4)
>C8 C12 C11 H6 H7 H8 H9 C7 C4 C3 C2 C1 C6 C5 H16 H15 H14 H13 H12 H10
>H11 H1 C9 H2 H3 C10 H4 H5 N1 H23 C13 C24 H18 H20 H21 H17 C14 O1 H28 H22
>C15 C19 H24 C17 H25 C18 O2 H19 C20 H26 C16 H27
>%FLAG CHARGE
>%FORMAT(5E16.8)
> -1.22089410E+00 -2.00263077E+00 2.09793340E+00 1.72947849E+00 1.73148295E+00
> 1.70323838E+00 1.50206419E+00 -5.65802415E-01 -1.94778165E+00 -2.42557035E+00
> -2.21182277E+00 -2.13036909E+00 -2.22330282E+00 -2.43869041E+00 2.36835233E+00
> 2.60998003E+00 2.66227803E+00 2.61562894E+00 2.37400124E+00 1.20412958E+00
> 1.21160073E+00 1.11812033E+00 -2.00645745E+00 1.69339834E+00 1.53285988E+00
> 2.09100893E+00 1.71654066E+00 1.81020328E+00 -1.24347153E+01 8.52275193E+00
> 2.12144017E+00 -2.22822284E+00 1.79106987E+00 1.12358702E+00 1.10900918E+00
> 1.85521236E+00 3.65703339E+00 -1.15995873E+01 8.24158184E+00 1.32895234E+00
> -3.98922592E+00 -9.96942033E-01 2.58282880E+00 -3.86658984E+00 2.83046986E+00
> 3.06480864E+00 -8.64793913E+00 7.96606067E+00 -2.71913161E+00 3.11583108E+00
> -1.63381142E+00 2.42921481E+00
>%FLAG MASS
>%FORMAT(5E16.8)
> 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00
> 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.20100000E+01
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> 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
> 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00
> 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.40100000E+01 1.00800000E+00
> 1.20100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
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> 1.20100000E+01 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
> 1.20100000E+01 1.60000000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
> 1.20100000E+01 1.00800000E+00
>%FLAG ATOM_TYPE_INDEX
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> 1 1 1 2 2 3 3 1 4 4
> 4 4 4 4 5 5 5 5 5 3
> 3 3 1 3 3 1 2 2 6 7
> 1 1 3 3 3 2 1 8 9 10
> 4 4 5 4 5 4 8 9 4 5
> 4 5
>%FLAG NUMBER_EXCLUDED_ATOMS
>%FORMAT(10I8)
> 20 17 16 7 6 5 4 14 13 10
> 7 7 5 6 1 1 1 1 1 3
> 2 4 8 5 4 8 4 3 11 4
> 12 8 4 3 2 4 10 5 2 3
> 9 8 4 7 3 6 4 1 3 2
> 1 1
>%FLAG NONBONDED_PARM_INDEX
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> 1 2 4 7 11 16 22 29 37 46
> 2 3 5 8 12 17 23 30 38 47
> 4 5 6 9 13 18 24 31 39 48
> 7 8 9 10 14 19 25 32 40 49
> 11 12 13 14 15 20 26 33 41 50
> 16 17 18 19 20 21 27 34 42 51
> 22 23 24 25 26 27 28 35 43 52
> 29 30 31 32 33 34 35 36 44 53
> 37 38 39 40 41 42 43 44 45 54
> 46 47 48 49 50 51 52 53 54 55
>%FLAG RESIDUE_LABEL
>%FORMAT(20a4)
>MOL
>%FLAG RESIDUE_POINTER
>%FORMAT(10I8)
> 1
>%FLAG BOND_FORCE_CONSTANT
>%FORMAT(5E16.8)
> 3.44300000E+02 4.78400000E+02 3.69600000E+02 3.86100000E+02 3.14100000E+02
> 3.35900000E+02 3.23500000E+02 3.37300000E+02 3.03100000E+02 3.38700000E+02
> 3.69000000E+02 2.93600000E+02
>%FLAG BOND_EQUIL_VALUE
>%FORMAT(5E16.8)
> 1.08700000E+00 1.38700000E+00 9.74000000E-01 1.36200000E+00 1.42600000E+00
> 1.09300000E+00 1.51300000E+00 1.09200000E+00 1.53500000E+00 1.09100000E+00
> 1.03300000E+00 1.49900000E+00
>%FLAG ANGLE_FORCE_CONSTANT
>%FORMAT(5E16.8)
> 4.85000000E+01 6.98000000E+01 4.89000000E+01 6.72000000E+01 4.68000000E+01
> 5.10000000E+01 6.72000000E+01 4.71000000E+01 6.38000000E+01 4.60000000E+01
> 3.94000000E+01 6.32000000E+01 4.64000000E+01 6.77000000E+01 4.64000000E+01
> 6.25000000E+01 4.62000000E+01 6.60000000E+01 4.90000000E+01 3.90000000E+01
> 6.28000000E+01 4.70000000E+01
>%FLAG ANGLE_EQUIL_VALUE
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> 2.09457053E+00 2.09334880E+00 1.91061275E+00 2.09387240E+00 1.93644364E+00
> 1.91776860E+00 1.97169930E+00 1.88774893E+00 2.10539158E+00 1.95023174E+00
> 1.89106506E+00 1.93085858E+00 1.92073567E+00 1.90991462E+00 1.92108473E+00
> 2.00032271E+00 1.92178286E+00 1.90118797E+00 1.88338560E+00 1.93277844E+00
> 1.93103311E+00 1.92248100E+00
>%FLAG DIHEDRAL_FORCE_CONSTANT
>%FORMAT(5E16.8)
> 3.62500000E+00 9.00000000E-01 0.00000000E+00 1.66666667E-01 1.55555556E-01
> 1.60000000E-01 2.50000000E-01 1.50000000E-01 2.00000000E-01 2.50000000E-01
> 1.80000000E-01 1.10000000E+00
>%FLAG DIHEDRAL_PERIODICITY
>%FORMAT(5E16.8)
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
> 3.00000000E+00 1.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00
> 3.00000000E+00 2.00000000E+00
>%FLAG DIHEDRAL_PHASE
>%FORMAT(5E16.8)
> 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
> 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00
> 0.00000000E+00 3.14159400E+00
>%FLAG SOLTY
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> 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
> 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
>%FLAG LENNARD_JONES_ACOEF
>%FORMAT(5E16.8)
> 1.04308023E+06 2.27401052E+04 2.01823541E+02 9.71708117E+04 1.41077189E+03
> 7.51607703E+03 9.24822270E+05 2.01619733E+04 8.61541883E+04 8.19971662E+05
> 8.59947003E+04 1.21014911E+03 6.55825601E+03 7.62451550E+04 5.71629601E+03
> 9.95480466E+05 2.01791425E+04 8.96776989E+04 8.82619071E+05 7.91627154E+04
> 9.44293233E+05 2.56678134E+03 9.14716912E+00 1.07193646E+02 2.27577561E+03
> 8.90987508E+01 2.12601181E+03 1.39982777E-01 7.91544157E+05 1.45985502E+04
> 6.82786631E+04 7.01803794E+05 6.00750218E+04 7.44975864E+05 1.40467023E+03
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> 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
> 6.78771368E+04 8.79040886E+02 4.98586848E+03 6.01816484E+04 4.33325458E+03
> 6.20665997E+04 5.94667300E+01 4.66922514E+04 0.00000000E+00 3.25969625E+03
>%FLAG LENNARD_JONES_BCOEF
>%FORMAT(5E16.8)
> 6.75612247E+02 6.13981767E+01 3.56012899E+00 1.26919150E+02 9.41257003E+00
> 2.17257828E+01 5.99015525E+02 5.44372326E+01 1.12529845E+02 5.31102864E+02
> 1.18043746E+02 8.61880722E+00 2.00642027E+01 1.04660679E+02 1.85196588E+01
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> 8.01323529E+02 2.06278363E+01 7.57919667E-01 2.59456373E+00 1.82891803E+01
> 2.33864085E+00 2.09604198E+01 9.37598976E-02 6.93079947E+02 5.79323581E+01
> 1.25287818E+02 6.14502845E+02 1.16187983E+02 7.50714425E+02 1.79702257E+01
> 6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
> 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
> 1.06076943E+02 7.42992380E+00 1.76949863E+01 9.40505980E+01 1.63092814E+01
> 1.13252061E+02 1.93248820E+00 1.03606917E+02 0.00000000E+00 1.43076527E+01
>%FLAG BONDS_INC_HYDROGEN
>%FORMAT(10I8)
> 150 153 1 144 147 1 138 141 3 129
> 132 1 123 126 1 111 114 3 108 117
> 6 93 96 8 93 99 8 93 102 8
> 90 105 10 84 87 11 75 78 10 75
> 81 10 66 69 8 66 72 8 39 42
> 1 36 45 1 33 48 1 30 51 1
> 27 54 1 21 57 8 21 60 8 6
> 9 10 6 12 10 3 15 8 3 18
> 8 0 63 8
>%FLAG BONDS_WITHOUT_HYDROGEN
>%FORMAT(10I8)
> 144 150 2 135 138 4 135 144 2 129
> 135 2 123 129 2 120 123 2 120 150
> 2 108 111 5 108 120 7 90 93 9
> 90 108 9 84 90 12 75 84 12 66
> 75 9 36 39 2 33 36 2 30 33
> 2 27 30 2 24 27 2 24 39 2
> 21 24 7 6 84 12 3 6 9 0
> 3 9 0 21 9 0 66 9
>%FLAG ANGLES_INC_HYDROGEN
>%FORMAT(10I8)
> 147 144 150 1 144 150 153 1 135 138
> 141 3 135 144 147 1 132 129 135 1
> 126 123 129 1 123 129 132 1 120 123
> 126 1 120 150 153 1 117 108 120 5
> 111 108 117 6 108 111 114 8 105 90
> 108 10 99 93 102 11 96 93 99 11
> 96 93 102 11 93 90 105 10 90 93
> 96 13 90 93 99 13 90 93 102 13
> 90 108 117 15 87 84 90 17 84 90
> 105 19 81 75 84 19 78 75 81 20
> 78 75 84 19 75 84 87 17 72 66
> 75 13 69 66 72 11 69 66 75 13
> 66 75 78 10 66 75 81 10 63 0
> 66 13 57 21 60 11 39 36 45 1
> 36 33 48 1 36 39 42 1 33 30
> 51 1 33 36 45 1 30 27 54 1
> 30 33 48 1 27 30 51 1 24 21
> 57 22 24 21 60 22 24 27 54 1
> 24 39 42 1 21 0 63 13 15 3
> 18 11 12 6 84 19 9 6 12 20
> 9 6 84 19 6 3 15 13 6 3
> 18 13 6 84 87 17 3 0 63 13
> 3 6 9 10 3 6 12 10 0 3
> 15 13 0 3 18 13 0 21 57 13
> 0 21 60 13 0 66 69 13 0 66
> 72 13
>%FLAG ANGLES_WITHOUT_HYDROGEN
>%FORMAT(10I8)
> 138 135 144 2 135 144 150 4 129 135
> 138 2 129 135 144 4 123 120 150 4
> 123 129 135 4 120 123 129 4 120 150
> 144 4 111 108 120 7 108 120 123 9
> 108 120 150 9 93 90 108 12 90 108
> 111 14 90 108 120 16 84 90 93 18
> 84 90 108 18 75 84 90 21 66 75
> 84 18 33 36 39 4 30 33 36 4
> 27 24 39 4 27 30 33 4 24 27
> 30 4 24 39 36 4 21 0 66 12
> 21 24 27 9 21 24 39 9 6 84
> 75 21 6 84 90 21 3 0 21 12
> 3 0 66 12 3 6 84 18 0 3
> 6 12 0 21 24 16 0 66 75 12
>%FLAG DIHEDRALS_INC_HYDROGEN
>%FORMAT(10I8)
> 147 144 150 153 1 141 138 135 144 2
> 138 135 144 147 1 135 144 150 153 1
> 132 129 135 138 1 132 129 135 144 1
> 129 135 138 141 2 129 135 144 147 1
> 126 123 120 150 1 126 123 129 132 1
> 126 123 129 135 1 123 120 150 153 1
> 120 123 129 132 1 120 150 144 147 1
> 117 108 120 123 3 117 108 120 150 3
> 114 111 108 117 4 114 111 108 120 4
> 108 120 123 126 1 108 120 150 153 1
> 105 90 108 111 5 105 90 108 117 5
> 105 90 108 120 5 102 93 90 105 5
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> 90 108 111 114 7 90 108 -111 114 6
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> 78 75 84 90 5 75 84 90 105 5
> 72 66 75 78 5 72 66 75 81 5
> 72 66 75 84 5 69 66 75 78 5
> 69 66 75 81 5 69 66 75 84 5
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> 51 30 27 54 1 48 33 30 51 1
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> 39 36 33 48 1 39 24 21 57 3
> 39 24 21 60 3 39 24 27 54 1
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> 12 6 84 87 5 12 6 84 90 5
> 9 6 3 15 5 9 6 3 18 5
> 9 6 84 75 5 9 6 84 87 5
> 9 6 84 90 5 63 0 3 6 6
> 6 84 75 78 5 6 84 75 81 5
> 6 84 90 105 5 3 0 21 57 6
> 3 0 21 60 6 3 0 66 69 6
> 3 0 66 72 6 3 6 84 87 5
> 0 3 6 9 5 0 3 6 12 5
> 0 66 75 78 5 0 66 75 81 5
> 120 144 -150 -153 12 135 150 -144 -147 12
> 123 135 -129 -132 12 120 129 -123 -126 12
> 24 36 -39 -42 12 33 39 -36 -45 12
> 30 36 -33 -48 12 27 33 -30 -51 12
> 24 30 -27 -54 12
>%FLAG DIHEDRALS_WITHOUT_HYDROGEN
>%FORMAT(10I8)
> 138 135 144 150 1 129 123 120 150 1
> 129 135 -144 150 1 123 120 150 144 1
> 123 129 135 138 1 123 129 -135 144 1
> 120 123 129 135 1 120 150 -144 135 1
> 111 108 120 123 3 111 108 120 150 3
> 108 120 123 129 1 108 120 150 144 1
> 93 90 108 111 5 93 90 108 120 5
> 90 108 120 123 3 90 108 120 150 3
> 84 90 108 111 5 84 90 108 120 5
> 75 84 90 93 5 75 84 90 108 5
> 66 75 84 90 5 30 27 24 39 1
> 30 33 -36 39 1 27 24 39 36 1
> 27 30 -33 36 1 66 0 21 24 5
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> 21 24 39 36 1 21 0 3 6 9
> 21 0 -3 6 10 21 0 -3 6 11
> 66 0 3 6 9 66 0 -3 6 10
> 66 0 -3 6 11 6 84 -75 66 5
> 6 84 90 93 5 6 84 90 108 5
> 3 0 21 24 5 3 0 66 75 9
> 3 0 -66 75 10 3 0 -66 75 11
> 3 6 -84 75 5 3 6 84 90 5
> 0 3 6 84 5 0 21 24 27 3
> 0 21 24 39 3 0 66 -75 84 5
> 123 150 -120 -108 12 21 27 -24 -39 12
>%FLAG EXCLUDED_ATOMS_LIST
>%FORMAT(10I8)
> 2 3 4 5 6 7 8 9 10 14
> 20 21 22 23 24 25 26 27 28 29
> 3 4 5 6 7 8 9 20 21 22
> 23 24 25 26 29 30 31 4 5 6
> 7 8 22 23 26 27 28 29 30 31
> 32 36 37 5 6 7 26 29 30 31
> 6 7 26 29 30 31 7 8 22 23
> 29 8 22 23 29 9 10 11 13 14
> 15 19 20 21 22 23 24 25 26 10
> 11 12 13 14 15 16 18 19 20 21
> 22 23 11 12 13 14 15 17 18 19
> 20 21 12 13 14 16 17 18 19 13
> 14 15 16 17 18 19 14 15 16 17
> 18 15 16 17 19 20 21 16 17 18
> 19 0 21 22 23 22 23 23 24 25
> 26 24 25 26 27 28 29 30 31 25
> 26 27 28 29 26 27 28 29 27 28
> 29 30 31 32 36 37 28 29 30 31
> 29 30 31 30 31 32 33 34 35 36
> 37 38 40 41 31 32 36 37 32 33
> 34 35 36 37 38 39 40 41 42 51
> 33 34 35 36 37 38 40 41 34 35
> 36 37 35 36 37 36 37 37 38 40
> 41 38 39 40 41 42 43 44 49 51
> 52 39 40 41 42 51 40 41 41 42
> 51 42 43 44 45 46 49 50 51 52
> 43 44 45 46 47 49 51 52 44 45
> 46 51 45 46 47 48 49 50 51 46
> 47 49 47 48 49 50 51 52 48 49
> 50 51 49 50 51 52 51 52 52 0
>%FLAG HBOND_ACOEF
>%FORMAT(5E16.8)
>
>%FLAG HBOND_BCOEF
>%FORMAT(5E16.8)
>
>%FLAG HBCUT
>%FORMAT(5E16.8)
>
>%FLAG AMBER_ATOM_TYPE
>%FORMAT(20a4)
>c3 c3 c3 hx hx hc hc c3 ca ca ca ca ca ca ha ha ha ha ha hc
>hc hc c3 hc hc c3 hx hx n4 hn c3 c3 hc hc hc hx c3 oh ho h1
>ca ca ha ca ha ca oh ho ca ha ca ha
>%FLAG TREE_CHAIN_CLASSIFICATION
>%FORMAT(20a4)
>M 3 B E E E E 3 B B B B S S E E E E E E
>E E M E E M E E M E M 3 E E E E M S E E
>M B E B E B S E S E M E
>%FLAG JOIN_ARRAY
>%FORMAT(10I8)
> 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
>%FLAG IROTAT
>%FORMAT(10I8)
> 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
>%FLAG RADIUS_SET
>%FORMAT(1a80)
>modified Bondi radii (mbondi)
>%FLAG RADII
>%FORMAT(5E16.8)
> 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
> 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00
> 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.30000000E+00
> 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
> 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
> 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.55000000E+00 1.30000000E+00
> 1.70000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
> 1.30000000E+00 1.70000000E+00 1.50000000E+00 8.00000000E-01 1.30000000E+00
> 1.70000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
> 1.70000000E+00 1.50000000E+00 8.00000000E-01 1.70000000E+00 1.30000000E+00
> 1.70000000E+00 1.30000000E+00
>%FLAG SCREEN
>%FORMAT(5E16.8)
> 7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
> 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01
> 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01
> 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
> 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
> 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01
> 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
> 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
> 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
> 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
> 7.20000000E-01 8.50000000E-01
>
>

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
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Received on Wed Sep 27 2006 - 06:07:21 PDT
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