attached mail follows:
Hi amber users,
I'm trying to do a normal mode calculation (with nmode, Amber 8) with
the flag ipol = 1, but the program crashes quickly with a "segmentation
fault" error message. if I turn it to 0, I don't have this message
anymore. I've already done a minimisation with sander with that flag on
(using the ff02 force field), and it worked fine. I've attached my input
files to this message.
thanks in advance if you have any suggestion in this regard
guillaume
calcul des modes normaux
&data
ntrun=1,
nprint=1,
nvect=324,
dielc = 1.0, scnb = 2.0, scee = 1.0,
ntx=1,
ntxO=1,
nsave=2,
ivform=2,
maxcyc=5,
drms=0.1,
idiel = 1,
ipol = 1,
cut=12
/
MOL
108
-0.0780850 0.1992555 0.3497002 1.4726264 0.1750084 0.3809129
2.1429918 1.5325199 0.2235076 3.3263333 1.5617196 -0.4059119
1.6034480 2.5330850 0.6358715 -0.5201054 -0.7045486 0.5942762
1.8173660 -0.1995018 1.3487505 1.8507204 -0.4604045 -0.4235399
-0.4274257 0.9243536 1.0114722 -0.4354426 0.4953141 -0.5796194
4.0408578 2.8169367 -0.7495567 3.2302423 3.7833479 -1.6232663
3.5408604 5.0835115 -1.5134980 2.3727714 3.4134130 -2.3964238
3.8010371 0.6990190 -0.6100037 5.3855961 2.4694662 -1.4314261
6.2395933 1.5672461 -0.5870582 6.0136198 1.2710506 0.5556726
7.2851028 1.0216036 -1.1759715 4.2372175 3.3646034 0.1784213
5.9582026 3.3758606 -1.6299267 5.1984664 1.9820093 -2.3903278
7.5150796 1.2308590 -2.1277673 7.8434388 0.4130183 -0.6050747
2.8500155 6.1669906 -2.2464577 3.7116778 7.4337437 -2.3689792
3.3747313 8.3056862 -3.3301737 4.6370052 7.6591634 -1.6178145
4.2704684 5.3671705 -0.8788325 1.5139193 6.4465772 -1.5069570
0.5792187 7.3266548 -2.2809321 0.7107841 7.6036625 -3.4468224
-0.4171899 7.8477198 -1.5945956 2.6481174 5.8397768 -3.2724509
1.7177270 6.9019780 -0.5362320 0.9844393 5.5110800 -1.3213222
-0.5359013 7.6531499 -0.6216728 -1.0072267 8.5184522 -2.0805716
3.9171516 9.6773672 -3.4573632 3.0281634 10.5945559 -4.3093664
2.6244071 11.7400810 -3.7334279 2.6851876 10.3337679 -5.4416356
2.5199022 8.0916513 -3.8404211 5.3490958 9.6494640 -4.0395139
5.9951650 11.0541378 -3.9720679 7.3980118 11.0858671 -4.4988311
7.7194468 11.5896920 -5.5442200 8.3320590 10.5254538 -3.7529625
3.9538323 10.1178789 -2.4567070 5.3211639 9.2942218 -5.0743402
5.9583834 8.9425258 -3.4709517 5.9982281 11.4296191 -2.9473605
5.4175813 11.7516892 -4.5761958 8.0968565 10.1069677 -2.8744721
9.2661330 10.5626751 -4.1118214 1.5947700 12.6481853 -4.3065545
1.8973133 14.1387678 -4.1005983 2.9486944 14.5993300 -4.7998485
1.2980968 14.8628119 -3.3338777 2.9453469 11.9170712 -2.7969667
0.1815128 12.2611571 -3.7975816 -0.2931753 10.8990892 -4.3686448
-1.6309854 10.4723387 -3.8393033 -1.8099156 9.9416481 -2.7720914
-2.6802895 10.6738387 -4.6124644 1.5924714 12.5397944 -5.3956446
-0.5295540 13.0300418 -4.1052088 0.1772110 12.2362614 -2.7038522
0.4012926 10.1087341 -4.0928867 -0.3205957 10.9353338 -5.4593398
-2.5707274 11.1009816 -5.5137947 -3.5471472 10.2961003 -4.2837830
3.6364974 15.9125446 -4.6453350 2.8625425 17.2067260 -4.9781373
1.5729464 17.2775583 -4.6234805 3.3643160 18.1346749 -5.5760457
3.4341495 13.9104971 -5.3489075 4.9536007 15.8537568 -5.4537868
5.7963193 14.6696065 -5.0829660 5.8720548 14.1914711 -3.9810063
6.4413168 14.0840906 -6.0730008 3.8828740 16.0298311 -3.5854633
5.5547579 16.7452922 -5.2732721 4.7249254 15.8227216 -6.5208516
6.3969512 14.4501315 -7.0014506 6.9995470 13.2690540 -5.8459259
0.6806189 18.4364753 -4.8753553 1.2236370 19.8225493 -4.5028649
0.9028625 20.8574037 -5.0297317 1.5456789 19.9974899 -3.2801122
1.2041639 16.4802844 -4.1113664 -0.6975598 18.2199606 -4.2128109
-1.4161816 16.9267447 -4.5739608 -1.7955645 16.0343012 -3.5686024
-2.4934925 14.8700884 -3.8880060 -2.7910821 14.5880378 -5.2143057
-2.4074071 15.4613064 -6.2224658 -1.7275587 16.6370836 -5.9044092
-3.4679238 13.4567494 -5.5145197 0.5336841 18.5024339 -5.9560395
-1.3499633 19.0559101 -4.4768914 -0.5683473 18.2673705 -3.1284774
-1.5492688 16.2474383 -2.5300362 -1.4468379 17.3297089 -6.6950621
-2.7868233 14.1845209 -3.0980722 -2.6580658 15.2292629 -7.2532774
-3.7822846 13.0906089 -4.6702518 1.5205300 20.9646621 -3.4150510
%VERSION VERSION_STAMP = V0001.000 DATE = 06/12/08 17:31:33
%FLAG TITLE
%FORMAT(20a4)
MOL
%FLAG POINTERS
%FORMAT(10I8)
108 11 49 59 106 79 225 137 0 0
573 1 59 79 137 17 33 23 13 0
0 0 0 0 0 0 0 0 108 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
N1 C1 C2 N2 O1 H1 H2 H3 H4 H5 C3 C4 N3 O2 H6 C5 C6 O3 N4 H7
H8 H9 H10 H11 C7 C8 N5 O4 H12 C9 C10 O5 N6 H13 H14 H15 H16 H17 C11 C12
N7 O6 H18 C13 C14 C15 O7 N8 H19 H20 H21 H22 H23 H24 H25 C16 C17 N9 O8 H26
C18 C19 C20 O9 N10 H27 H28 H29 H30 H31 H32 H33 C21 C22 N11 O10 H34 C23 C24 O11
N12 H35 H36 H37 H38 H39 C25 C26 O12 O13 H40 C27 C28 C29 C30 C31 C32 C33 O14 H41
H42 H43 H44 H45 H46 H47 H48 H49
%FLAG CHARGE
%FORMAT(5E16.8)
-1.53777990E+01 6.86980710E-01 1.20267180E+01 -9.64688562E+00 -1.04960448E+01
8.59363668E+00 2.39987691E+00 2.13018687E+00 8.72848170E+00 8.59545891E+00
1.11338253E+00 1.20267180E+01 -1.02901328E+01 -1.09916914E+01 6.02975907E+00
-3.25996947E+00 1.19046286E+01 -1.08987576E+01 -1.22472078E+01 1.91151927E+00
1.94249718E+00 1.33569459E+00 5.85300276E+00 6.12087057E+00 1.03320441E+00
1.19939179E+01 -1.03338663E+01 -1.12613814E+01 6.14091510E+00 -3.34014759E+00
1.21633852E+01 -1.17278723E+01 -1.22326300E+01 1.96436394E+00 1.24093863E+00
1.49058414E+00 5.64162408E+00 6.78051783E+00 1.08604908E+00 1.19884512E+01
-1.05270227E+01 -1.06126675E+01 6.57096138E+00 -1.42680609E+00 -3.12330222E+00
1.25296535E+01 -1.14946268E+01 -1.21834298E+01 1.15164936E+00 1.37031696E+00
1.12613814E+00 1.29013884E+00 1.50333975E+00 5.80380255E+00 5.92589196E+00
7.56225450E-01 1.21615630E+01 -1.03138218E+01 -1.09698246E+01 5.90402520E+00
-1.34116128E+00 -3.07410201E+00 1.24713421E+01 -1.19228509E+01 -1.22289855E+01
1.65276261E+00 1.31382783E+00 1.25369424E+00 1.62907362E+00 1.20996072E+00
6.04798137E+00 5.85118053E+00 1.14071598E+00 1.19738733E+01 -1.06272454E+01
-1.09752913E+01 5.87851398E+00 -3.09050208E+00 1.19483621E+01 -1.15547604E+01
-1.25059645E+01 1.66734045E+00 1.96436394E+00 1.24276086E+00 5.66349084E+00
6.57825030E+00 1.53796212E+00 1.13944042E+01 -1.00732874E+01 -1.00951542E+01
6.47802765E+00 -6.41424960E-01 -2.19214269E+00 -1.21724964E+00 -4.18566231E+00
2.30329872E+00 -2.95383483E+00 -1.48329522E+00 -9.28790631E+00 1.46325069E+00
1.31747229E+00 1.15347159E+00 2.58938883E+00 2.61672228E+00 2.43449928E+00
2.70054486E+00 7.76087757E+00 8.19456831E+00
%FLAG MASS
%FORMAT(5E16.8)
1.40100000E+01 1.20100000E+01 1.20100000E+01 1.40100000E+01 1.60000000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.20100000E+01 1.20100000E+01 1.40100000E+01 1.60000000E+01 1.00800000E+00
1.20100000E+01 1.20100000E+01 1.60000000E+01 1.40100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.20100000E+01 1.40100000E+01 1.60000000E+01 1.00800000E+00 1.20100000E+01
1.20100000E+01 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01
1.40100000E+01 1.60000000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01
1.20100000E+01 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.20100000E+01 1.20100000E+01 1.40100000E+01 1.60000000E+01 1.00800000E+00
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.40100000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.40100000E+01
1.60000000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.60000000E+01
1.40100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.60000000E+01
1.00800000E+00 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 3 1 4 5 6 6 5 5
2 3 1 4 5 2 3 4 1 7
8 8 5 5 2 3 1 4 5 2
3 4 1 7 8 8 5 5 2 3
1 4 5 2 2 3 4 1 7 8
8 8 8 5 5 2 3 1 4 5
2 2 3 4 1 7 8 8 8 8
5 5 2 3 1 4 5 2 3 4
1 7 8 8 5 5 2 3 4 9
5 2 3 3 3 3 3 3 9 7
8 8 10 10 10 10 11 11
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
9 10 12 13 4 4 3 2 1 1
13 13 13 4 2 8 7 5 4 2
1 1 1 1 13 13 13 4 2 8
7 5 4 2 1 1 1 1 14 13
13 4 2 9 10 8 5 4 2 3
2 1 1 1 1 14 13 13 4 2
9 10 8 5 4 2 3 2 1 1
1 1 13 13 13 4 2 8 7 5
4 2 1 1 1 1 12 9 4 3
2 10 12 10 8 8 6 6 3 2
1 1 1 1 1 1 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 29 37 46
56 2 3 5 8 12 17 23 30 38
47 57 4 5 6 9 13 18 24 31
39 48 58 7 8 9 10 14 19 25
32 40 49 59 11 12 13 14 15 20
26 33 41 50 60 16 17 18 19 20
21 27 34 42 51 61 22 23 24 25
26 27 28 35 43 52 62 29 30 31
32 33 34 35 36 44 53 63 37 38
39 40 41 42 43 44 45 54 64 46
47 48 49 50 51 52 53 54 55 65
56 57 58 59 60 61 62 63 64 65
66
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
MOL
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
2.93600000E+02 3.69000000E+02 3.28300000E+02 3.38700000E+02 4.78200000E+02
6.48000000E+02 3.30600000E+02 4.10200000E+02 3.03100000E+02 3.35900000E+02
3.37300000E+02 4.66400000E+02 3.69600000E+02 3.23500000E+02 4.78400000E+02
3.44300000E+02 3.86100000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.49900000E+00 1.03300000E+00 1.50800000E+00 1.09100000E+00 1.34500000E+00
1.21400000E+00 1.46000000E+00 1.00900000E+00 1.53500000E+00 1.09300000E+00
1.09200000E+00 1.30600000E+00 9.74000000E-01 1.51300000E+00 1.38700000E+00
1.08700000E+00 1.36200000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
6.58000000E+01 4.90000000E+01 4.62000000E+01 6.79000000E+01 6.80000000E+01
4.74000000E+01 6.39000000E+01 4.92000000E+01 7.58000000E+01 6.67000000E+01
6.59000000E+01 4.98000000E+01 4.05000000E+01 3.90000000E+01 4.60000000E+01
6.38000000E+01 4.64000000E+01 4.76000000E+01 4.64000000E+01 4.72000000E+01
3.94000000E+01 3.97000000E+01 6.32000000E+01 6.98000000E+01 6.25000000E+01
5.12000000E+01 7.74000000E+01 6.38000000E+01 4.70000000E+01 6.72000000E+01
4.85000000E+01 6.98000000E+01 4.89000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.94674108E+00 1.88338560E+00 1.92178286E+00 2.00974750E+00 2.14867576E+00
1.89612651E+00 2.11795796E+00 2.06751792E+00 2.12982620E+00 1.94709015E+00
1.95703853E+00 1.90799476E+00 1.88687626E+00 1.93277844E+00 2.03819637E+00
1.92911325E+00 1.92073567E+00 1.87902228E+00 1.92108473E+00 1.91427794E+00
1.89106506E+00 2.05687140E+00 1.93085858E+00 1.95826026E+00 2.00032271E+00
1.87396082E+00 2.14466150E+00 2.10539158E+00 1.92248100E+00 2.09387240E+00
2.09457053E+00 2.09334880E+00 1.91061275E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
0.00000000E+00 2.50000000E+00 1.55555556E-01 8.00000000E-01 8.50000000E-01
5.30000000E-01 1.50000000E-01 5.00000000E-01 0.00000000E+00 1.70000000E+00
2.00000000E+00 2.00000000E+00 7.00000000E-02 1.00000000E-01 8.00000000E-02
1.60000000E-01 1.50000000E-01 2.30000000E+00 1.90000000E+00 3.62500000E+00
9.00000000E-01 1.05000000E+01 1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00
1.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00
2.00000000E+00 1.00000000E+00 2.00000000E+00 4.00000000E+00 3.00000000E+00
3.00000000E+00 3.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 3.14159400E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
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
0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
9.44293233E+05 9.95480466E+05 1.04308023E+06 8.82619071E+05 9.24822270E+05
8.19971662E+05 6.06829342E+05 6.47841731E+05 5.74393458E+05 3.79876399E+05
2.12601181E+03 2.56678134E+03 2.27577561E+03 1.02595236E+03 1.39982777E-01
2.01791425E+04 2.27401052E+04 2.01619733E+04 1.12780457E+04 9.14716912E+00
2.01823541E+02 6.20665997E+04 6.78771368E+04 6.01816484E+04 3.69471530E+04
5.94667300E+01 8.79040886E+02 3.25969625E+03 8.96776989E+04 9.71708117E+04
8.61541883E+04 5.44261042E+04 1.07193646E+02 1.41077189E+03 4.98586848E+03
7.51607703E+03 7.44975864E+05 7.91544157E+05 7.01803794E+05 4.71003287E+05
1.40467023E+03 1.45985502E+04 4.66922514E+04 6.82786631E+04 5.81803229E+05
7.91627154E+04 8.59947003E+04 7.62451550E+04 4.77908183E+04 8.90987508E+01
1.21014911E+03 4.33325458E+03 6.55825601E+03 6.00750218E+04 5.71629601E+03
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
0.00000000E+00
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
8.01323529E+02 7.36907417E+02 6.75612247E+02 6.53361429E+02 5.99015525E+02
5.31102864E+02 6.77220874E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
2.09604198E+01 2.06278363E+01 1.82891803E+01 1.53505284E+01 9.37598976E-02
6.45756063E+01 6.13981767E+01 5.44372326E+01 5.08951803E+01 7.57919667E-01
3.56012899E+00 1.13252061E+02 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.93248820E+00 7.42992380E+00 1.43076527E+01 1.36131731E+02 1.26919150E+02
1.12529845E+02 1.11805549E+02 2.59456373E+00 9.41257003E+00 1.76949863E+01
2.17257828E+01 7.50714425E+02 6.93079947E+02 6.14502845E+02 6.29300710E+02
1.79702257E+01 5.79323581E+01 1.03606917E+02 1.25287818E+02 6.99746810E+02
1.26451907E+02 1.18043746E+02 1.04660679E+02 1.03580945E+02 2.33864085E+00
8.61880722E+00 1.63092814E+01 2.00642027E+01 1.16187983E+02 1.85196588E+01
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
0.00000000E+00
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 15 2 0 24 2 0 27 2 3
18 4 3 21 4 9 42 8 30 57
10 36 84 8 45 60 11 45 63 11
54 66 8 54 69 8 72 99 10 78
126 8 87 102 11 87 105 11 96 108
8 96 111 8 114 144 10 120 177 8
129 147 11 129 150 11 132 153 11 132
156 11 141 159 8 141 162 8 165 195
10 171 228 8 180 198 11 180 201 11
183 204 11 183 207 11 192 210 8 192
213 8 216 243 10 222 270 8 231 246
11 231 249 11 240 252 8 240 255 8
258 297 10 267 321 13 273 300 11 273
303 11 279 306 16 282 312 16 288 315
16 291 309 16 294 318 13
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 1 3 6 3 6 9 5 6
12 6 9 30 7 30 33 3 30 45
9 33 36 5 33 39 6 36 72 7
45 48 3 48 51 6 48 54 5 72
75 3 72 87 9 75 78 5 75 81
6 78 114 7 87 90 3 90 93 6
90 96 5 114 117 3 114 129 9 117
120 5 117 123 6 120 165 7 129 132
9 132 135 3 135 138 6 135 141 5
165 168 3 165 180 9 168 171 5 168
174 6 171 216 7 180 183 9 183 186
3 186 189 6 186 192 5 216 219 3
216 231 9 219 222 5 219 225 6 222
258 7 231 234 3 234 237 6 234 240
5 258 261 3 258 273 9 261 264 6
261 267 12 273 276 14 276 279 15 276
291 15 279 282 15 282 285 15 285 288
15 285 294 17 288 291 15
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 3 18 2 0 3 21 2 3 0
15 3 3 0 24 3 3 0 27 3
6 3 18 6 6 3 21 6 6 9
42 8 9 30 57 12 15 0 24 13
15 0 27 13 18 3 21 14 24 0
27 13 30 9 42 15 30 45 60 17
30 45 63 17 33 30 57 18 33 36
84 8 36 72 99 12 45 30 57 19
48 45 60 20 48 45 63 20 48 54
66 8 48 54 69 8 60 45 63 21
66 54 69 22 72 36 84 15 72 87
102 17 72 87 105 17 75 72 99 18
75 78 126 8 78 114 144 12 87 72
99 19 90 87 102 20 90 87 105 20
90 96 108 8 90 96 111 8 102 87
105 21 108 96 111 22 114 78 126 15
114 129 147 17 114 129 150 17 117 114
144 18 117 120 177 8 120 165 195 12
129 114 144 19 129 132 153 17 129 132
156 17 132 129 147 17 132 129 150 17
135 132 153 20 135 132 156 20 135 141
159 8 135 141 162 8 147 129 150 21
153 132 156 21 159 141 162 22 165 120
177 15 165 180 198 17 165 180 201 17
168 165 195 18 168 171 228 8 171 216
243 12 180 165 195 19 180 183 204 17
180 183 207 17 183 180 198 17 183 180
201 17 186 183 204 20 186 183 207 20
186 192 210 8 186 192 213 8 198 180
201 21 204 183 207 21 210 192 213 22
216 171 228 15 216 231 246 17 216 231
249 17 219 216 243 18 219 222 270 8
222 258 297 12 231 216 243 19 234 231
246 20 234 231 249 20 234 240 252 8
234 240 255 8 246 231 249 21 252 240
255 22 258 222 270 15 258 273 300 17
258 273 303 17 261 258 297 18 261 267
321 26 273 258 297 19 276 273 300 29
276 273 303 29 276 279 306 31 276 291
309 31 279 282 312 31 282 279 306 31
285 282 312 31 285 288 315 31 285 294
318 33 288 291 309 31 291 288 315 31
300 273 303 21
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 6 1 3 6 9 4 3 6
12 5 6 9 30 7 9 6 12 9
9 30 33 10 9 30 45 11 30 33
36 4 30 33 39 5 30 45 48 16
33 30 45 16 33 36 72 7 36 33
39 9 36 72 75 10 36 72 87 11
45 48 51 5 45 48 54 4 51 48
54 9 72 75 78 4 72 75 81 5
72 87 90 16 75 72 87 16 75 78
114 7 78 75 81 9 78 114 117 10
78 114 129 11 87 90 93 5 87 90
96 4 93 90 96 9 114 117 120 4
114 117 123 5 114 129 132 23 117 114
129 16 117 120 165 7 120 117 123 9
120 165 168 10 120 165 180 11 129 132
135 16 132 135 138 5 132 135 141 4
138 135 141 9 165 168 171 4 165 168
174 5 165 180 183 23 168 165 180 16
168 171 216 7 171 168 174 9 171 216
219 10 171 216 231 11 180 183 186 16
183 186 189 5 183 186 192 4 189 186
192 9 216 219 222 4 216 219 225 5
216 231 234 16 219 216 231 16 219 222
258 7 222 219 225 9 222 258 261 10
222 258 273 11 231 234 237 5 231 234
240 4 237 234 240 9 258 261 264 5
258 261 267 24 258 273 276 25 261 258
273 16 264 261 267 27 273 276 279 28
273 276 291 28 276 279 282 30 276 291
288 30 279 276 291 30 279 282 285 30
282 285 288 30 282 285 294 32 285 288
291 30 288 285 294 32
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
3 6 9 42 2 15 0 3 6 3
24 0 3 6 3 27 0 3 6 3
6 9 30 57 9 9 6 3 18 1
9 6 3 21 1 9 30 45 60 3
9 30 45 63 3 12 6 3 18 1
12 6 3 21 1 12 6 9 42 12
12 6 -9 42 2 15 0 3 18 3
15 0 3 21 3 24 0 3 18 3
27 0 3 18 3 24 0 3 21 3
27 0 3 21 3 30 33 36 84 2
33 30 9 42 9 33 30 45 60 3
33 30 45 63 3 33 36 72 99 9
36 33 30 57 1 36 72 87 102 3
36 72 87 105 3 39 33 30 57 4
39 33 -30 57 15 39 33 36 84 12
39 33 -36 84 2 42 9 30 45 9
42 9 30 57 9 45 48 54 66 2
45 48 54 69 2 48 45 30 57 3
51 48 45 60 4 51 48 -45 60 15
51 48 45 63 4 51 48 -45 63 15
51 48 54 66 12 51 48 -54 66 2
51 48 54 69 12 51 48 -54 69 2
54 48 45 60 1 54 48 45 63 1
57 30 45 60 3 57 30 45 63 3
72 75 78 126 2 75 72 36 84 9
75 72 87 102 3 75 72 87 105 3
75 78 114 144 9 78 75 72 99 1
78 114 129 147 3 78 114 129 150 3
81 75 72 99 4 81 75 -72 99 15
81 75 78 126 12 81 75 -78 126 2
84 36 72 87 9 84 36 72 99 9
87 90 96 108 2 87 90 96 111 2
90 87 72 99 3 93 90 87 102 4
93 90 -87 102 15 93 90 87 105 4
93 90 -87 105 15 93 90 96 108 12
93 90 -96 108 2 93 90 96 111 12
93 90 -96 111 2 96 90 87 102 1
96 90 87 105 1 99 72 87 102 3
99 72 87 105 3 114 117 120 177 2
114 129 132 153 16 114 129 132 156 16
117 114 78 126 9 117 114 129 147 3
117 114 129 150 3 117 120 165 195 9
120 117 114 144 1 120 165 180 198 3
120 165 180 201 3 123 117 114 144 4
123 117 -114 144 15 123 117 120 177 12
123 117 -120 177 2 126 78 114 129 9
126 78 114 144 9 132 129 114 144 3
132 135 141 159 2 132 135 141 162 2
135 132 129 147 3 135 132 129 150 3
138 135 132 153 4 138 135 -132 153 15
138 135 132 156 4 138 135 -132 156 15
138 135 141 159 12 138 135 -141 159 2
138 135 141 162 12 138 135 -141 162 2
141 135 132 153 1 141 135 132 156 1
144 114 129 147 3 144 114 129 150 3
147 129 132 153 17 147 129 132 156 17
150 129 132 153 17 150 129 132 156 17
165 168 171 228 2 165 180 183 204 16
165 180 183 207 16 168 165 120 177 9
168 165 180 198 3 168 165 180 201 3
168 171 216 243 9 171 168 165 195 1
171 216 231 246 3 171 216 231 249 3
174 168 165 195 4 174 168 -165 195 15
174 168 171 228 12 174 168 -171 228 2
177 120 165 180 9 177 120 165 195 9
183 180 165 195 3 183 186 192 210 2
183 186 192 213 2 186 183 180 198 3
186 183 180 201 3 189 186 183 204 4
189 186 -183 204 15 189 186 183 207 4
189 186 -183 207 15 189 186 192 210 12
189 186 -192 210 2 189 186 192 213 12
189 186 -192 213 2 192 186 183 204 1
192 186 183 207 1 195 165 180 198 3
195 165 180 201 3 198 180 183 204 17
198 180 183 207 17 201 180 183 204 17
201 180 183 207 17 216 219 222 270 2
219 216 171 228 9 219 216 231 246 3
219 216 231 249 3 219 222 258 297 9
222 219 216 243 1 222 258 273 300 3
222 258 273 303 3 225 219 216 243 4
225 219 -216 243 15 225 219 222 270 12
225 219 -222 270 2 228 171 216 231 9
228 171 216 243 9 231 234 240 252 2
231 234 240 255 2 234 231 216 243 3
237 234 231 246 4 237 234 -231 246 15
237 234 231 249 4 237 234 -231 249 15
237 234 240 252 12 237 234 -240 252 2
237 234 240 255 12 237 234 -240 255 2
240 234 231 246 1 240 234 231 249 1
243 216 231 246 3 243 216 231 249 3
258 261 267 321 18 261 258 222 270 9
261 258 273 300 3 261 258 273 303 3
264 261 258 297 4 264 261 -258 297 15
264 261 267 321 19 264 261 -267 321 18
267 261 258 297 1 270 222 258 273 9
270 222 258 297 9 273 276 279 306 20
273 276 291 309 20 276 273 258 297 3
276 279 282 312 20 276 291 288 315 20
279 276 273 300 9 279 276 273 303 9
279 276 291 309 20 282 285 288 315 20
282 285 294 318 21 285 282 279 306 20
285 288 291 309 20 288 285 282 312 20
288 285 294 318 21 291 276 273 300 9
291 276 273 303 9 291 276 279 306 20
294 285 282 312 20 294 285 288 315 20
297 258 273 300 3 297 258 273 303 3
306 279 282 312 20 309 291 288 315 20
6 30 -9 -42 23 33 72 -36 -84 23
48 66 -54 -69 23 75 114 -78 -126 23
90 108 -96 -111 23 117 165 -120 -177 23
135 159 -141 -162 23 168 216 -171 -228 23
186 210 -192 -213 23 219 258 -222 -270 23
234 252 -240 -255 23
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 6 9 1 0 3 6 12 1
3 6 9 30 2 6 9 30 33 4
6 9 -30 33 5 6 9 30 45 6
6 9 -30 45 7 6 9 -30 45 8
9 30 33 36 10 9 30 -33 36 11
9 30 33 39 1 9 30 45 48 3
12 6 9 30 2 30 33 36 72 2
30 45 48 51 1 30 45 48 54 13
30 45 -48 54 14 33 30 45 48 3
33 36 72 75 4 33 36 -72 75 5
33 36 72 87 6 33 36 -72 87 9
33 36 -72 87 7 33 36 -72 87 8
36 33 30 45 13 36 33 -30 45 14
36 72 75 78 10 36 72 -75 78 11
36 72 75 81 1 36 72 87 90 3
39 33 30 45 1 39 33 36 72 2
72 75 78 114 2 72 87 90 93 1
72 87 90 96 13 72 87 -90 96 14
75 72 87 90 3 75 78 114 117 4
75 78 -114 117 5 75 78 114 129 6
75 78 -114 129 9 75 78 -114 129 7
75 78 -114 129 8 78 75 72 87 13
78 75 -72 87 14 78 114 117 120 10
78 114 -117 120 11 78 114 117 123 1
78 114 129 132 3 81 75 72 87 1
81 75 78 114 2 114 117 120 165 2
114 129 132 135 3 117 114 129 132 3
117 120 165 168 4 117 120 -165 168 5
117 120 165 180 6 117 120 -165 180 9
117 120 -165 180 7 117 120 -165 180 8
120 117 114 129 13 120 117 -114 129 14
120 165 168 171 10 120 165 -168 171 11
120 165 168 174 1 120 165 180 183 3
123 117 114 129 1 123 117 120 165 2
129 132 135 138 1 129 132 135 141 13
129 132 -135 141 14 165 168 171 216 2
165 180 183 186 3 168 165 180 183 3
168 171 216 219 4 168 171 -216 219 5
168 171 216 231 6 168 171 -216 231 9
168 171 -216 231 7 168 171 -216 231 8
171 168 165 180 13 171 168 -165 180 14
171 216 219 222 10 171 216 -219 222 11
171 216 219 225 1 171 216 231 234 3
174 168 165 180 1 174 168 171 216 2
180 183 186 189 1 180 183 186 192 13
180 183 -186 192 14 216 219 222 258 2
216 231 234 237 1 216 231 234 240 13
216 231 -234 240 14 219 216 231 234 3
219 222 258 261 4 219 222 -258 261 5
219 222 258 273 6 219 222 -258 273 9
219 222 -258 273 7 219 222 -258 273 8
222 219 216 231 13 222 219 -216 231 14
222 258 261 264 1 222 258 261 267 1
222 258 273 276 3 225 219 216 231 1
225 219 222 258 2 258 273 276 279 9
258 273 276 291 9 261 258 273 276 3
264 261 258 273 1 267 261 258 273 1
273 276 279 282 20 273 276 291 288 20
276 279 282 285 20 276 291 -288 285 20
279 276 291 288 20 279 282 -285 288 20
279 282 285 294 20 282 279 276 291 20
282 285 -288 291 20 291 288 285 294 20
3 9 -6 -12 22 30 36 -33 -39 22
45 54 -48 -51 22 72 78 -75 -81 22
87 96 -90 -93 22 114 120 -117 -123 22
132 141 -135 -138 22 165 171 -168 -174 22
183 192 -186 -189 22 216 222 -219 -225 22
231 240 -234 -237 22 258 264 -261 -267 23
279 291 -276 -273 23
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 3
4 5 6 7 8 9 10 11 15 4
5 6 7 8 9 10 11 12 15 16
20 5 7 8 11 12 13 14 15 16
17 20 21 22 7 8 11 15 7 8
9 10 8 9 10 9 10 10 0 12
13 14 15 16 17 18 19 20 21 22
25 29 13 14 15 16 17 20 21 22
25 26 29 30 34 14 16 20 25 26
27 28 29 30 31 34 35 36 16 20
25 29 16 20 17 18 19 20 21 22
23 24 18 19 20 21 22 23 24 19
21 22 23 24 21 22 23 24 21 22
22 0 24 0 26 27 28 29 30 31
32 33 34 35 36 39 43 27 28 29
30 31 34 35 36 39 40 43 44 49
28 30 34 39 40 41 42 43 44 45
49 50 51 30 34 39 43 30 34 31
32 33 34 35 36 37 38 32 33 34
35 36 37 38 33 35 36 37 38 35
36 37 38 35 36 36 0 38 0 40
41 42 43 44 45 46 49 50 51 52
53 56 60 41 42 43 44 45 49 50
51 56 57 60 61 66 42 44 49 56
57 58 59 60 61 62 66 67 68 44
49 56 60 44 49 45 46 47 48 49
50 51 52 53 46 47 48 49 50 51
52 53 54 55 47 48 50 51 52 53
54 55 48 52 53 54 55 52 53 54
55 50 51 51 52 53 52 53 53 0
55 0 57 58 59 60 61 62 63 66
67 68 69 70 73 77 58 59 60 61
62 66 67 68 73 74 77 78 82 59
61 66 73 74 75 76 77 78 79 82
83 84 61 66 73 77 61 66 62 63
64 65 66 67 68 69 70 63 64 65
66 67 68 69 70 71 72 64 65 67
68 69 70 71 72 65 69 70 71 72
69 70 71 72 67 68 68 69 70 69
70 70 0 72 0 74 75 76 77 78
79 80 81 82 83 84 87 91 75 76
77 78 79 82 83 84 87 88 91 92
100 76 78 82 87 88 89 90 91 92
93 100 101 102 78 82 87 91 78 82
79 80 81 82 83 84 85 86 80 81
82 83 84 85 86 81 83 84 85 86
83 84 85 86 83 84 84 0 86 0
88 89 90 91 92 93 94 98 100 101
102 108 89 90 91 92 93 100 101 102
108 90 92 100 108 92 100 108 92 100
93 94 95 97 98 100 101 102 103 104
94 95 96 97 98 100 101 102 103 104
105 106 95 96 97 98 99 101 102 103
104 105 96 97 98 99 103 105 106 107
97 98 99 103 104 105 106 107 98 99
104 105 106 107 99 101 102 103 104 106
105 106 107 101 102 102 0 105 106 0
0 0 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
n4 c3 c n o hn hx hx hn hn c3 c n o hn c3 c o n h1
hc hc hn hn c3 c n o hn c3 c o n h1 hc hc hn hn c3 c
n o hn c3 c3 c o n h1 hc hc hc hc hn hn c3 c n o hn
c3 c3 c o n h1 hc hc hc hc hn hn c3 c n o hn c3 c o
n h1 hc hc hn hn c3 c o oh hn c3 ca ca ca ca ca ca oh h1
hc hc ha ha ha ha ho ho
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA
%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 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 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 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 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 RADII
%FORMAT(5E16.8)
1.55000000E+00 1.70000000E+00 1.70000000E+00 1.55000000E+00 1.50000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.70000000E+00 1.55000000E+00 1.50000000E+00 1.30000000E+00
1.70000000E+00 1.70000000E+00 1.50000000E+00 1.55000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.70000000E+00 1.55000000E+00 1.50000000E+00 1.30000000E+00 1.70000000E+00
1.70000000E+00 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00
1.55000000E+00 1.50000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00
1.70000000E+00 1.50000000E+00 1.55000000E+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 1.70000000E+00 1.55000000E+00 1.50000000E+00 1.30000000E+00
1.70000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.55000000E+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 1.70000000E+00 1.55000000E+00
1.50000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00
1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.50000000E+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 1.50000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00 8.00000000E-01 8.00000000E-01
%FLAG SCREEN
%FORMAT(5E16.8)
7.90000000E-01 7.20000000E-01 7.20000000E-01 7.90000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01
7.90000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01
7.20000000E-01 8.50000000E-01 7.90000000E-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 7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-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 7.20000000E-01 7.90000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01
7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 7.20000000E-01 7.20000000E-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 8.50000000E-01 8.50000000E-01
%FLAG POLARIZABILITY
%FORMAT(5E16.8)
5.30000000E-01 8.78000000E-01 6.16000000E-01 5.30000000E-01 4.34000000E-01
1.61000000E-01 1.35000000E-01 1.35000000E-01 1.61000000E-01 1.61000000E-01
8.78000000E-01 6.16000000E-01 5.30000000E-01 4.34000000E-01 1.61000000E-01
8.78000000E-01 6.16000000E-01 4.34000000E-01 5.30000000E-01 1.35000000E-01
1.35000000E-01 1.35000000E-01 1.61000000E-01 1.61000000E-01 8.78000000E-01
6.16000000E-01 5.30000000E-01 4.34000000E-01 1.61000000E-01 8.78000000E-01
6.16000000E-01 4.34000000E-01 5.30000000E-01 1.35000000E-01 1.35000000E-01
1.35000000E-01 1.61000000E-01 1.61000000E-01 8.78000000E-01 6.16000000E-01
5.30000000E-01 4.34000000E-01 1.61000000E-01 8.78000000E-01 8.78000000E-01
6.16000000E-01 4.34000000E-01 5.30000000E-01 1.35000000E-01 1.35000000E-01
1.35000000E-01 1.35000000E-01 1.35000000E-01 1.61000000E-01 1.61000000E-01
8.78000000E-01 6.16000000E-01 5.30000000E-01 4.34000000E-01 1.61000000E-01
8.78000000E-01 8.78000000E-01 6.16000000E-01 4.34000000E-01 5.30000000E-01
1.35000000E-01 1.35000000E-01 1.35000000E-01 1.35000000E-01 1.35000000E-01
1.61000000E-01 1.61000000E-01 8.78000000E-01 6.16000000E-01 5.30000000E-01
4.34000000E-01 1.61000000E-01 8.78000000E-01 6.16000000E-01 4.34000000E-01
5.30000000E-01 1.35000000E-01 1.35000000E-01 1.35000000E-01 1.61000000E-01
1.61000000E-01 8.78000000E-01 6.16000000E-01 4.34000000E-01 4.65000000E-01
1.61000000E-01 8.78000000E-01 3.60000000E-01 3.60000000E-01 3.60000000E-01
3.60000000E-01 3.60000000E-01 3.60000000E-01 4.65000000E-01 1.35000000E-01
1.35000000E-01 1.35000000E-01 1.35000000E-01 1.35000000E-01 1.35000000E-01
1.35000000E-01 1.35000000E-01 1.35000000E-01
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Jun 18 2008 - 06:07:32 PDT
